2025-05-10 22:01
ftp://ftp.de.debian.org/debian/pool/main/g/gmap/gmap_2024-11-20+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-1022-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: beb3362 (2025-05-10 14:33:23 +0200)
count: 4271 4217
elapsed-time: 91.2 90.9
head-timing-info:

old-timing-info:

head results:
gmap-2024-11-20/src/access.c:124:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:150:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:186:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:197:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:317:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IPC_STAT [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:374:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:448:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:487:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:518:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:582:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:679:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IPC_CREAT [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:898:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/access.c:898:5: portability: %lu in format string (no. 2) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/access.c:895:30: style: Redundant pointer operation on 'shmid' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/access.c:895:40: style: Redundant pointer operation on 'key' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/access.c:118:25: style: Parameter 'dest_file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:118:42: style: Parameter 'source_file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:145:26: style: Parameter 'file1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:145:39: style: Parameter 'file2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:183:22: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:194:25: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:369:9: style: Variable 'memory' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/access.c:432:26: style: Parameter 'memory' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:471:39: style: Parameter 'memory' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:512:44: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:577:45: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/access.c:402:29: style: Variable 'nattached' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/atoiindex.c:130:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/atoiindex.c:420:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/atoiindex.c:462:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/atoiindex.c:658:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/atoiindex.c:829:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/atoiindex.c:992:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/atoiindex.c:1188:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/atoiindex.c:1020:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/atoiindex.c:1021:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/atoiindex.c:434:23: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/atoiindex.c:434:39: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/atoiindex.c:623:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/atoiindex.c:623:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/atoiindex.c:794:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/atoiindex.c:794:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/atoiindex.c:611:16: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/atoiindex.c:973:9: style: Unused variable: sequence_fp [unusedVariable]
gmap-2024-11-20/src/altsplice.c:87:29: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/altsplice.c:945:11: style:inconclusive: Function 'Altsplice_resolve_qstart' argument 4 names different: declaration 'medial_nmismatches_L' definition 'medial_nmismatches_H'. [funcArgNamesDifferent]
gmap-2024-11-20/src/altsplice.h:146:11: note: Function 'Altsplice_resolve_qstart' argument 4 names different: declaration 'medial_nmismatches_L' definition 'medial_nmismatches_H'.
gmap-2024-11-20/src/altsplice.c:945:11: note: Function 'Altsplice_resolve_qstart' argument 4 names different: declaration 'medial_nmismatches_L' definition 'medial_nmismatches_H'.
gmap-2024-11-20/src/altsplice.c:191:31: style: Parameter 'univdiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:210:32: style: Parameter 'univdiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:233:15: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:234:18: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:288:13: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:289:16: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:343:14: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:344:17: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:511:12: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:512:15: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:460:48: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:460:82: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:461:20: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:461:55: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:462:20: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:462:47: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:463:20: style: Parameter 'snp_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:463:48: style: Parameter 'snp_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:463:75: style: Parameter 'snp_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:545:46: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:545:80: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:546:25: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:546:60: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:547:25: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:547:52: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:549:25: style: Parameter 'mask_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1057:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1057:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1058:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1058:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1059:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1059:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1090:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1090:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1091:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1091:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1092:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1092:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1474:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1474:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1475:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1475:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1476:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1476:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1506:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1506:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1507:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1507:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1508:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:1508:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/altsplice.c:787:14: style: Variable 'starti' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/altsplice.c:815:14: style: Variable 'starti' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/altsplice.c:758:10: style: Unused variable: best_prob [unusedVariable]
gmap-2024-11-20/src/altsplice.c:758:21: style: Unused variable: prob [unusedVariable]
gmap-2024-11-20/src/altsplice.c:759:8: style: Unused variable: outer_accept_p [unusedVariable]
gmap-2024-11-20/src/altsplice.c:987:14: style: Variable 'startj' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/altsplice.c:1015:14: style: Variable 'startj' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/altsplice.c:958:10: style: Unused variable: best_prob [unusedVariable]
gmap-2024-11-20/src/altsplice.c:958:21: style: Unused variable: prob [unusedVariable]
gmap-2024-11-20/src/altsplice.c:959:8: style: Unused variable: outer_accept_p [unusedVariable]
gmap-2024-11-20/src/altsplice.c:1156:7: style: Unused variable: best_insertlength [unusedVariable]
gmap-2024-11-20/src/altsplice.c:1159:10: style: Unused variable: best_prob [unusedVariable]
gmap-2024-11-20/src/altsplice.c:1159:21: style: Unused variable: prob [unusedVariable]
gmap-2024-11-20/src/altsplice.c:1160:8: style: Unused variable: outer_accept_p [unusedVariable]
gmap-2024-11-20/src/altsplice.c:1431:10: style: Variable 'prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/altsplice.c:1510:10: style: Variable 'prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/auxinfo.c:181:19: style:inconclusive: Function 'Auxinfo_append' argument 1 names different: declaration 'new' definition 'first'. [funcArgNamesDifferent]
gmap-2024-11-20/src/auxinfo.h:53:19: note: Function 'Auxinfo_append' argument 1 names different: declaration 'new' definition 'first'.
gmap-2024-11-20/src/auxinfo.c:181:19: note: Function 'Auxinfo_append' argument 1 names different: declaration 'new' definition 'first'.
gmap-2024-11-20/src/auxinfo.c:181:28: style:inconclusive: Function 'Auxinfo_append' argument 2 names different: declaration 'old' definition 'second'. [funcArgNamesDifferent]
gmap-2024-11-20/src/auxinfo.h:53:26: note: Function 'Auxinfo_append' argument 2 names different: declaration 'old' definition 'second'.
gmap-2024-11-20/src/auxinfo.c:181:28: note: Function 'Auxinfo_append' argument 2 names different: declaration 'old' definition 'second'.
gmap-2024-11-20/src/bigendian.c:32:14: error: Buffer is accessed out of bounds: buf [bufferAccessOutOfBounds]
gmap-2024-11-20/src/bigendian.c:512:32: portability:inconclusive: Casting from double * to unsigned char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
gmap-2024-11-20/src/bigendian.c:536:24: portability:inconclusive: Casting from double * to unsigned char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
gmap-2024-11-20/src/bigendian.c:41:43: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bigendian.c:98:29: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bigendian.c:221:39: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bigendian.c:512:26: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-access.c:2123:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-incr.c:8374:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-incr.c:8454:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-read.c:13309:41: style: Parameter 'columnar' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-read.c:14705:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-read.c:14908:53: style: Parameter 'bitpackpages' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-read.c:15255:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-read.c:15261:59: style: Variable 'vertical' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-read.c:15604:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitpack64-write.c:130:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-write.c:155:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-write.c:4389:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-write.c:4440:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-write.c:4651:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-write.c:4822:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-write.c:5378:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-write.c:5555:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitvector.c:99:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitvector.c:116:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bitpack64-readtwo.c:14224:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:425:67: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
gmap-2024-11-20/src/bitvector.c:168:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:168:24: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:198:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:290:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:310:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:331:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:356:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bitvector.c:385:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/block.c:430:46: style: Redundant pointer operation on 'nfwdhits' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/block.c:432:46: style: Redundant pointer operation on 'nrevhits' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/block.c:446:46: style: Redundant pointer operation on 'nfwdhits' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/block.c:448:46: style: Redundant pointer operation on 'nrevhits' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/boyer-moore.c:448:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:74:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:136:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:191:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:289:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:416:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:655:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:716:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:772:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:855:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:918:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bytecoding.c:987:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/boyer-moore.c:201:39: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/boyer-moore.c:290:46: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/boyer-moore.c:465:29: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/boyer-moore.c:465:56: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/boyer-moore.c:466:14: style: Parameter 'bad_char_shift' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/boyer-moore.c:208:44: warning: Uninitialized variable: f [uninitvar]
gmap-2024-11-20/src/bzip2.c:42:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bzip2.c:99:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bzip2.c:135:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/bzip2.c:61:3: style:inconclusive: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/bzip2.c:38:7: style: Unused variable: error [unusedVariable]
gmap-2024-11-20/src/bzip2.c:39:9: style: Unused variable: fp [unusedVariable]
gmap-2024-11-20/src/changepoint.c:26:62: style: Parameter 'matchscores' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/changepoint.c:134:65: style: Parameter 'matchscores' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:67:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:40:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:40:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:67:3: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:71:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:39:19: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:39:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:71:10: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:72:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:40:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:40:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:72:10: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:78:42: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:77:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:77:14: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:78:42: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:79:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:77:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:77:14: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:79:10: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:100:44: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:99:16: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:99:16: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:100:44: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:101:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:99:16: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:99:16: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:101:12: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:105:49: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:104:19: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:104:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:105:49: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:106:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:104:19: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:104:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:106:10: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:131:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:108:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:108:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:131:3: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:134:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:108:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:108:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:134:10: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:184:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:157:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:157:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:184:3: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:188:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:156:19: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:156:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:188:10: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:189:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2024-11-20/src/bytecoding.c:157:14: note: Assuming allocation function fails
gmap-2024-11-20/src/bytecoding.c:157:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2024-11-20/src/bytecoding.c:189:10: note: Null pointer dereference
gmap-2024-11-20/src/bytecoding.c:927:78: style:inconclusive: Function 'Bytecoding_lcpchilddc_lcp_next' argument 3 names different: declaration 'lcpchilddc' definition 'bytes'. [funcArgNamesDifferent]
gmap-2024-11-20/src/bytecoding.h:49:20: note: Function 'Bytecoding_lcpchilddc_lcp_next' argument 3 names different: declaration 'lcpchilddc' definition 'bytes'.
gmap-2024-11-20/src/bytecoding.c:927:78: note: Function 'Bytecoding_lcpchilddc_lcp_next' argument 3 names different: declaration 'lcpchilddc' definition 'bytes'.
gmap-2024-11-20/src/bytecoding.c:28:25: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:28:42: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:28:57: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:28:75: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:89:31: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:89:48: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:89:63: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:89:89: style: Parameter 'bytes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:90:11: style: Parameter 'exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:145:41: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:145:56: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:145:74: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:265:36: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:265:53: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:265:68: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:265:86: style: Parameter 'child' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:266:24: style: Parameter 'discrim_chars' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:266:54: style: Parameter 'lcpbytes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:399:41: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:399:67: style: Parameter 'child_bytes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:399:95: style: Parameter 'discrim_chars' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:399:125: style: Parameter 'lcpbytes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:610:44: style: Parameter 'bytes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:663:51: style: Parameter 'bytes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:663:65: style: Parameter 'guide' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:727:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bytecoding.c:788:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bytecoding.c:800:73: style: Parameter 'guide' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:800:87: style: Parameter 'exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:802:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bytecoding.c:863:75: style: Parameter 'guide' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:863:89: style: Parameter 'exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:865:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bytecoding.c:927:92: style: Parameter 'child_guide' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:928:12: style: Parameter 'child_exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bytecoding.c:931:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/bytecoding.c:361:17: style: Variable 'bytes_ptr' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/bytecoding.c:447:17: style: Variable 'bytes_ptr' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/bitpack64-write.c:5624:17: error: Array 'last_block[64]' accessed at index 64, which is out of bounds. [arrayIndexOutOfBounds]
gmap-2024-11-20/src/bitpack64-write.c:5622:15: note: Assuming that condition 'i<=64' is not redundant
gmap-2024-11-20/src/bitpack64-write.c:5624:17: note: Array index out of bounds
gmap-2024-11-20/src/bitpack64-write.c:5396:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5396:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5424:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5424:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5458:5: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5458:5: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5574:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5574:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5603:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5603:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5645:5: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:5645:5: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/bitpack64-write.c:111:12: style: Parameter 'horizontal' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:146:13: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4455:56: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4623:37: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4623:53: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4744:45: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4794:46: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4794:62: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4794:78: style: Parameter 'packsizes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:5348:42: style: Parameter 'pagesfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:5348:59: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:5348:75: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:5517:51: style: Parameter 'pagesfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:5517:68: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:5517:84: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:5518:16: style: Parameter 'packsizes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/bitpack64-write.c:4135:22: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/bitpack64-write.c:4734:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/bitpack64-write.c:4908:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/bitpack64-write.c:5507:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/bitpack64-write.c:5694:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/chrom.c:134:21: style:inconclusive: Redundant condition: The condition '*p != '\0'' is redundant since '*p >= '0'' is sufficient. [redundantCondition]
gmap-2024-11-20/src/chrom.c:74:56: style:inconclusive: Function 'Chrom_altlocp' argument 2 names different: declaration 'alt_scaffold_stop' definition 'alt_scaffold_end'. [funcArgNamesDifferent]
gmap-2024-11-20/src/chrom.h:21:56: note: Function 'Chrom_altlocp' argument 2 names different: declaration 'alt_scaffold_stop' definition 'alt_scaffold_end'.
gmap-2024-11-20/src/chrom.c:74:56: note: Function 'Chrom_altlocp' argument 2 names different: declaration 'alt_scaffold_stop' definition 'alt_scaffold_end'.
gmap-2024-11-20/src/chrom.c:94:40: style: Parameter 'mitochondrial_string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/chrom.c:98:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/cmetindex.c:130:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/cmetindex.c:560:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/cmetindex.c:602:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/cmetindex.c:798:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/cmetindex.c:969:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/cmetindex.c:1132:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/cmetindex.c:1328:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/chimera.c:484:48: style: Parameter 'circularp' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/cmetindex.c:1160:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/cmetindex.c:1161:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/cmetindex.c:574:23: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/cmetindex.c:574:39: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/cmetindex.c:763:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/cmetindex.c:763:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/cmetindex.c:934:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/cmetindex.c:934:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/cmetindex.c:751:16: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/cmetindex.c:1113:9: style: Unused variable: sequence_fp [unusedVariable]
gmap-2024-11-20/src/compress-write.c:108:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/compress-write.c:271:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/compress-write.c:323:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/compress-write.c:545:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/compress-write.c:832:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/compress.c:163:17: style: Variable 'high_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:163:31: style: Variable 'low_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:163:44: style: Variable 'flags_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:307:17: style: Variable 'high_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:307:31: style: Variable 'low_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:307:44: style: Variable 'flags_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:343:17: style: Variable 'high_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:343:31: style: Variable 'low_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:343:44: style: Variable 'flags_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress.c:389:25: style: Parameter 'gbuffer' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/compress.c:533:25: style: Parameter 'gbuffer' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/compress.c:395:18: style: Variable 'in_counter' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/compress.c:539:18: style: Variable 'in_counter' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/compress-write.c:116:39: style: Checking if unsigned expression 'fread(&high,sizeof(unsigned int),1,sequence_fp)' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/compress-write.c:117:31: style: Checking if unsigned expression 'fread(&low,sizeof(unsigned int),1,sequence_fp)' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/compress-write.c:118:33: style: Checking if unsigned expression 'fread(&flags,sizeof(unsigned int),1,sequence_fp)' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/compress-write.c:240:54: style: Parameter 'Buffer' can be declared as const array [constParameter]
gmap-2024-11-20/src/compress-write.c:293:69: style: Parameter 'Buffer' can be declared as const array [constParameter]
gmap-2024-11-20/src/compress-write.c:540:16: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress-write.c:781:44: style: Parameter 'genomecomp' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/compress-write.c:808:9: style: Variable 'file' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/compress-write.c:975:37: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 991. [shiftTooManyBits]
gmap-2024-11-20/src/compress-write.c:991:17: note: Assuming that condition 'shift==0' is not redundant
gmap-2024-11-20/src/compress-write.c:983:33: note: Assignment to 'shift=32-current_pos'
gmap-2024-11-20/src/compress-write.c:975:37: note: Shift
gmap-2024-11-20/src/compress-write.c:1002:28: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 962. [shiftTooManyBits]
gmap-2024-11-20/src/compress-write.c:962:23: note: Assuming that condition 'current_pos==0' is not redundant
gmap-2024-11-20/src/compress-write.c:983:33: note: Assignment 'shift=32-current_pos', assigned value is 32
gmap-2024-11-20/src/compress-write.c:1002:28: note: Shift
gmap-2024-11-20/src/compress-write.c:1005:36: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 962. [shiftTooManyBits]
gmap-2024-11-20/src/compress-write.c:962:23: note: Assuming that condition 'current_pos==0' is not redundant
gmap-2024-11-20/src/compress-write.c:983:33: note: Assignment 'shift=32-current_pos', assigned value is 32
gmap-2024-11-20/src/compress-write.c:1005:36: note: Shift
gmap-2024-11-20/src/compress-write.c:814:21: style: Variable 'buffer_high' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/compress-write.c:814:37: style: Variable 'buffer_low' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/compress-write.c:816:76: style: Variable 'buffer_flags' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/cpuid.c:23:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/datadir.c:43:0: error: #error A default value for GMAPDB was not provided to configure.  Please do so, or edit the Makefile [preprocessorErrorDirective]
gmap-2024-11-20/src/datadir.c:43:2: error: #error A default value for GMAPDB was not provided to configure.  Please do so, or edit the Makefile [preprocessorErrorDirective]
gmap-2024-11-20/src/diag.c:76:13: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/diag.c:323:48: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/diag.c:323:68: style: Parameter 'genomicseg_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/concordance.c:152:26: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:167:26: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:182:30: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:197:30: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:458:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:458:57: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:458:75: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:477:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:477:57: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:477:75: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:496:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:496:57: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/concordance.c:496:75: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/doublelist.c:19:33: style:inconclusive: Function 'Doublelist_push' argument 2 names different: declaration 'index' definition 'elt'. [funcArgNamesDifferent]
gmap-2024-11-20/src/doublelist.h:8:42: note: Function 'Doublelist_push' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2024-11-20/src/doublelist.c:19:33: note: Function 'Doublelist_push' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2024-11-20/src/doublelist.c:28:33: style:inconclusive: Function 'Doublelist_pop' argument 2 names different: declaration 'index' definition 'elt'. [funcArgNamesDifferent]
gmap-2024-11-20/src/doublelist.h:9:42: note: Function 'Doublelist_pop' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2024-11-20/src/doublelist.c:28:33: note: Function 'Doublelist_pop' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2024-11-20/src/doublelist.c:167:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/doublelist.c:183:32: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog.c:212:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog.c:1171:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_cdna.c:98:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_cdna.c:1227:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_cdna.c:1276:39: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_cdna.c:787:43: style:inconclusive: Function 'Dynprog_cdna_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_cdna.h:18:43: note: Function 'Dynprog_cdna_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_cdna.c:787:43: note: Function 'Dynprog_cdna_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_cdna.c:1221:14: style: Variable 'finalscore' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/dynprog_end.c:1541:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_end.c:2142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_end.c:2543:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_end.c:2596:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_end.c:2644:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_end.c:2698:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_end.c:1572:62: style: Condition '*traceback_score<=0' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/dynprog_end.c:1558:22: note: Assignment '*traceback_score=0', assigned value is 0
gmap-2024-11-20/src/dynprog_end.c:1572:62: note: Condition '*traceback_score<=0' is always true
gmap-2024-11-20/src/dynprog_end.c:2171:62: style: Condition '*traceback_score<=0' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/dynprog_end.c:2158:22: note: Assignment '*traceback_score=0', assigned value is 0
gmap-2024-11-20/src/dynprog_end.c:2171:62: note: Condition '*traceback_score<=0' is always true
gmap-2024-11-20/src/dynprog_end.c:2829:43: style: Condition 'glength>0' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/dynprog_end.c:2789:15: note: Assuming that condition 'glength<=0' is not redundant
gmap-2024-11-20/src/dynprog_end.c:2829:43: note: Condition 'glength>0' is always true
gmap-2024-11-20/src/dynprog_end.c:3091:43: style: Condition 'glength>0' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/dynprog_end.c:3050:15: note: Assuming that condition 'glength<=0' is not redundant
gmap-2024-11-20/src/dynprog_end.c:3091:43: note: Condition 'glength>0' is always true
gmap-2024-11-20/src/dynprog_end.c:1562:35: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1562:55: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1562:68: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1613:40: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1613:60: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1613:73: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1613:89: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1613:100: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1881:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1881:58: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1881:71: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1881:87: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1881:98: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1891:39: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1891:59: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1891:72: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1891:88: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1891:99: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2162:35: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2162:55: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2162:68: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2210:40: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2210:60: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2210:73: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2210:89: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2210:100: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2462:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2462:58: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2462:71: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2462:87: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2462:98: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2471:39: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2471:59: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2471:72: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2471:88: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2471:99: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2804:33: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2804:50: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2804:70: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2804:83: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2805:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2805:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2915:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2915:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2915:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2916:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2916:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2916:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2916:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2920:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2933:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2933:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2933:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2934:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2934:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2934:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2934:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2938:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2968:37: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2968:54: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2968:74: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2968:87: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2969:9: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:2969:20: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3066:33: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3066:50: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3066:70: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3066:83: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3067:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3067:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3177:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3177:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3177:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3178:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3178:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3178:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3178:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3182:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3195:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3195:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3195:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3196:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3196:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3196:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3196:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3200:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3230:37: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3230:54: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3230:74: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3230:87: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3231:9: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:3231:20: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_end.c:1294:43: style:inconclusive: Function 'Dynprog_end5_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:26:43: note: Function 'Dynprog_end5_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:1294:43: note: Function 'Dynprog_end5_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:1296:11: style:inconclusive: Function 'Dynprog_end5_gap' argument 8 names different: declaration 'revsequence1' definition 'rev_rsequence'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:28:11: note: Function 'Dynprog_end5_gap' argument 8 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2024-11-20/src/dynprog_end.c:1296:11: note: Function 'Dynprog_end5_gap' argument 8 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2024-11-20/src/dynprog_end.c:1296:32: style:inconclusive: Function 'Dynprog_end5_gap' argument 9 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:28:31: note: Function 'Dynprog_end5_gap' argument 9 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:1296:32: note: Function 'Dynprog_end5_gap' argument 9 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:1297:9: style:inconclusive: Function 'Dynprog_end5_gap' argument 10 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:29:9: note: Function 'Dynprog_end5_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:1297:9: note: Function 'Dynprog_end5_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:1297:22: style:inconclusive: Function 'Dynprog_end5_gap' argument 11 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:29:22: note: Function 'Dynprog_end5_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:1297:22: note: Function 'Dynprog_end5_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:1297:35: style:inconclusive: Function 'Dynprog_end5_gap' argument 12 names different: declaration 'revoffset1' definition 'rev_roffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:29:35: note: Function 'Dynprog_end5_gap' argument 12 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2024-11-20/src/dynprog_end.c:1297:35: note: Function 'Dynprog_end5_gap' argument 12 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2024-11-20/src/dynprog_end.c:1297:52: style:inconclusive: Function 'Dynprog_end5_gap' argument 13 names different: declaration 'revoffset2' definition 'rev_goffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:29:51: note: Function 'Dynprog_end5_gap' argument 13 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2024-11-20/src/dynprog_end.c:1297:52: note: Function 'Dynprog_end5_gap' argument 13 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2024-11-20/src/dynprog_end.c:1653:54: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:37:54: note: Function 'Dynprog_end5_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:1653:54: note: Function 'Dynprog_end5_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:1657:13: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:41:13: note: Function 'Dynprog_end5_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:1657:13: note: Function 'Dynprog_end5_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:1657:26: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:41:26: note: Function 'Dynprog_end5_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:1657:26: note: Function 'Dynprog_end5_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:1657:39: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:41:39: note: Function 'Dynprog_end5_splicejunction' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2024-11-20/src/dynprog_end.c:1657:39: note: Function 'Dynprog_end5_splicejunction' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2024-11-20/src/dynprog_end.c:1657:56: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 16 names different: declaration 'revoffset2_anchor' definition 'rev_goffset_anchor'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:41:55: note: Function 'Dynprog_end5_splicejunction' argument 16 names different: declaration 'revoffset2_anchor' definition 'rev_goffset_anchor'.
gmap-2024-11-20/src/dynprog_end.c:1657:56: note: Function 'Dynprog_end5_splicejunction' argument 16 names different: declaration 'revoffset2_anchor' definition 'rev_goffset_anchor'.
gmap-2024-11-20/src/dynprog_end.c:1657:80: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 17 names different: declaration 'revoffset2_far' definition 'rev_goffset_far'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:41:78: note: Function 'Dynprog_end5_splicejunction' argument 17 names different: declaration 'revoffset2_far' definition 'rev_goffset_far'.
gmap-2024-11-20/src/dynprog_end.c:1657:80: note: Function 'Dynprog_end5_splicejunction' argument 17 names different: declaration 'revoffset2_far' definition 'rev_goffset_far'.
gmap-2024-11-20/src/dynprog_end.c:1924:43: style:inconclusive: Function 'Dynprog_end3_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:48:43: note: Function 'Dynprog_end3_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:1924:43: note: Function 'Dynprog_end3_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:1926:11: style:inconclusive: Function 'Dynprog_end3_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:50:11: note: Function 'Dynprog_end3_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2024-11-20/src/dynprog_end.c:1926:11: note: Function 'Dynprog_end3_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2024-11-20/src/dynprog_end.c:1926:28: style:inconclusive: Function 'Dynprog_end3_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:50:28: note: Function 'Dynprog_end3_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:1926:28: note: Function 'Dynprog_end3_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:1927:9: style:inconclusive: Function 'Dynprog_end3_gap' argument 10 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:51:9: note: Function 'Dynprog_end3_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:1927:9: note: Function 'Dynprog_end3_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:1927:22: style:inconclusive: Function 'Dynprog_end3_gap' argument 11 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:51:22: note: Function 'Dynprog_end3_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:1927:22: note: Function 'Dynprog_end3_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:1927:35: style:inconclusive: Function 'Dynprog_end3_gap' argument 12 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:51:35: note: Function 'Dynprog_end3_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_end.c:1927:35: note: Function 'Dynprog_end3_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_end.c:1927:48: style:inconclusive: Function 'Dynprog_end3_gap' argument 13 names different: declaration 'offset2' definition 'goffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:51:48: note: Function 'Dynprog_end3_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2024-11-20/src/dynprog_end.c:1927:48: note: Function 'Dynprog_end3_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2024-11-20/src/dynprog_end.c:2249:54: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:59:54: note: Function 'Dynprog_end3_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:2249:54: note: Function 'Dynprog_end3_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:2253:13: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:63:13: note: Function 'Dynprog_end3_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:2253:13: note: Function 'Dynprog_end3_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:2253:26: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:63:26: note: Function 'Dynprog_end3_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:2253:26: note: Function 'Dynprog_end3_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:2253:39: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 15 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:63:39: note: Function 'Dynprog_end3_splicejunction' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_end.c:2253:39: note: Function 'Dynprog_end3_splicejunction' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_end.c:2253:52: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 16 names different: declaration 'offset2_anchor' definition 'goffset_anchor'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:63:52: note: Function 'Dynprog_end3_splicejunction' argument 16 names different: declaration 'offset2_anchor' definition 'goffset_anchor'.
gmap-2024-11-20/src/dynprog_end.c:2253:52: note: Function 'Dynprog_end3_splicejunction' argument 16 names different: declaration 'offset2_anchor' definition 'goffset_anchor'.
gmap-2024-11-20/src/dynprog_end.c:2253:72: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 17 names different: declaration 'offset2_far' definition 'goffset_far'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:63:72: note: Function 'Dynprog_end3_splicejunction' argument 17 names different: declaration 'offset2_far' definition 'goffset_far'.
gmap-2024-11-20/src/dynprog_end.c:2253:72: note: Function 'Dynprog_end3_splicejunction' argument 17 names different: declaration 'offset2_far' definition 'goffset_far'.
gmap-2024-11-20/src/dynprog_end.c:2748:65: style:inconclusive: Function 'Dynprog_end5_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:91:65: note: Function 'Dynprog_end5_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:2748:65: note: Function 'Dynprog_end5_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:2751:13: style:inconclusive: Function 'Dynprog_end5_known' argument 11 names different: declaration 'revsequence1' definition 'rev_rsequence'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:94:13: note: Function 'Dynprog_end5_known' argument 11 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2024-11-20/src/dynprog_end.c:2751:13: note: Function 'Dynprog_end5_known' argument 11 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2024-11-20/src/dynprog_end.c:2751:34: style:inconclusive: Function 'Dynprog_end5_known' argument 12 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:94:33: note: Function 'Dynprog_end5_known' argument 12 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:2751:34: note: Function 'Dynprog_end5_known' argument 12 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:2752:11: style:inconclusive: Function 'Dynprog_end5_known' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:95:11: note: Function 'Dynprog_end5_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:2752:11: note: Function 'Dynprog_end5_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:2752:24: style:inconclusive: Function 'Dynprog_end5_known' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:95:24: note: Function 'Dynprog_end5_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:2752:24: note: Function 'Dynprog_end5_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:2752:37: style:inconclusive: Function 'Dynprog_end5_known' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:95:37: note: Function 'Dynprog_end5_known' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2024-11-20/src/dynprog_end.c:2752:37: note: Function 'Dynprog_end5_known' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2024-11-20/src/dynprog_end.c:2752:54: style:inconclusive: Function 'Dynprog_end5_known' argument 16 names different: declaration 'revoffset2' definition 'rev_goffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:95:53: note: Function 'Dynprog_end5_known' argument 16 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2024-11-20/src/dynprog_end.c:2752:54: note: Function 'Dynprog_end5_known' argument 16 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2024-11-20/src/dynprog_end.c:3009:65: style:inconclusive: Function 'Dynprog_end3_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:108:65: note: Function 'Dynprog_end3_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:3009:65: note: Function 'Dynprog_end3_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_end.c:3012:13: style:inconclusive: Function 'Dynprog_end3_known' argument 11 names different: declaration 'sequence1' definition 'rsequence'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:111:13: note: Function 'Dynprog_end3_known' argument 11 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2024-11-20/src/dynprog_end.c:3012:13: note: Function 'Dynprog_end3_known' argument 11 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2024-11-20/src/dynprog_end.c:3012:30: style:inconclusive: Function 'Dynprog_end3_known' argument 12 names different: declaration 'sequenceuc1' definition 'rsequenceuc'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:111:30: note: Function 'Dynprog_end3_known' argument 12 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:3012:30: note: Function 'Dynprog_end3_known' argument 12 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2024-11-20/src/dynprog_end.c:3013:11: style:inconclusive: Function 'Dynprog_end3_known' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:112:11: note: Function 'Dynprog_end3_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:3013:11: note: Function 'Dynprog_end3_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_end.c:3013:24: style:inconclusive: Function 'Dynprog_end3_known' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:112:24: note: Function 'Dynprog_end3_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:3013:24: note: Function 'Dynprog_end3_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_end.c:3013:37: style:inconclusive: Function 'Dynprog_end3_known' argument 15 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:112:37: note: Function 'Dynprog_end3_known' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_end.c:3013:37: note: Function 'Dynprog_end3_known' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_end.c:3013:50: style:inconclusive: Function 'Dynprog_end3_known' argument 16 names different: declaration 'offset2' definition 'goffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_end.h:112:50: note: Function 'Dynprog_end3_known' argument 16 names different: declaration 'offset2' definition 'goffset'.
gmap-2024-11-20/src/dynprog_end.c:3013:50: note: Function 'Dynprog_end3_known' argument 16 names different: declaration 'offset2' definition 'goffset'.
gmap-2024-11-20/src/dynprog_end.c:650:25: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_end.c:650:42: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_end.c:651:11: style: Parameter 'gsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_end.c:651:28: style: Parameter 'gsequence_alt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_end.c:1140:57: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_end.c:1141:36: style: Parameter 'genomesequencealt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_end.c:2722:50: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_end.c:2874:16: style: Variable 'jstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/dynprog_end.c:3136:16: style: Variable 'jstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/dynprog.c:176:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog.c:1798:47: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog.c:1798:66: style: Parameter 'gsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog.c:1798:83: style: Parameter 'gsequence_alt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2913:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_single.c:234:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_single.c:143:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:579:36: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:579:56: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:579:69: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:644:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:644:58: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:644:71: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:644:87: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:644:98: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_single.c:429:45: style:inconclusive: Function 'Dynprog_single_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_single.h:23:45: note: Function 'Dynprog_single_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_single.c:429:45: note: Function 'Dynprog_single_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2024-11-20/src/dynprog_single.c:430:24: style:inconclusive: Function 'Dynprog_single_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_single.h:25:24: note: Function 'Dynprog_single_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2024-11-20/src/dynprog_single.c:430:24: note: Function 'Dynprog_single_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2024-11-20/src/dynprog_single.c:430:41: style:inconclusive: Function 'Dynprog_single_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_single.h:25:41: note: Function 'Dynprog_single_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2024-11-20/src/dynprog_single.c:430:41: note: Function 'Dynprog_single_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2024-11-20/src/dynprog_single.c:431:11: style:inconclusive: Function 'Dynprog_single_gap' argument 10 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_single.h:26:11: note: Function 'Dynprog_single_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_single.c:431:11: note: Function 'Dynprog_single_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2024-11-20/src/dynprog_single.c:431:24: style:inconclusive: Function 'Dynprog_single_gap' argument 11 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_single.h:26:24: note: Function 'Dynprog_single_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_single.c:431:24: note: Function 'Dynprog_single_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2024-11-20/src/dynprog_single.c:431:37: style:inconclusive: Function 'Dynprog_single_gap' argument 12 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_single.h:26:37: note: Function 'Dynprog_single_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_single.c:431:37: note: Function 'Dynprog_single_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2024-11-20/src/dynprog_single.c:431:50: style:inconclusive: Function 'Dynprog_single_gap' argument 13 names different: declaration 'offset2' definition 'goffset'. [funcArgNamesDifferent]
gmap-2024-11-20/src/dynprog_single.h:26:50: note: Function 'Dynprog_single_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2024-11-20/src/dynprog_single.c:431:50: note: Function 'Dynprog_single_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2024-11-20/src/dynprog_single.c:171:35: style: Parameter 'rsequence_nreps' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:172:14: style: Parameter 'gsequence_nreps' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:299:50: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:347:12: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:347:29: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:347:61: style: Parameter 'gsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:347:78: style: Parameter 'gsequence_alt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:686:15: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:686:32: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:901:33: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_single.c:636:18: warning: Uninitialized variable: gsequence [uninitvar]
gmap-2024-11-20/src/dynprog_single.c:535:20: note: Assuming condition is true
gmap-2024-11-20/src/dynprog_single.c:636:18: note: Uninitialized variable: gsequence
gmap-2024-11-20/src/dynprog_single.c:358:27: style: Variable 'pairdistance_array_type' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/dynprog_single.c:640:14: style: Variable 'finalscore' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/ef64.c:51:21: style: Parameter 'bits' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/ef64.c:144:37: style: Parameter 'repetitive_oligos' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/ef64.c:393:52: style: Parameter 'endpoints' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/select64-common.h:65:17: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
gmap-2024-11-20/src/ef64.c:185:19: warning: Uninitialized variable: oligo [uninitvar]
gmap-2024-11-20/src/ef64.c:177:17: note: Assuming condition is false
gmap-2024-11-20/src/ef64.c:185:19: note: Uninitialized variable: oligo
gmap-2024-11-20/src/except.c:125:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/dynprog_genome.c:2738:5: style: Variable 'cL' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2024-11-20/src/dynprog_genome.c:2682:8: note: cL is assigned 'rL' here.
gmap-2024-11-20/src/dynprog_genome.c:2738:5: note: Variable 'cL' is assigned an expression that holds the same value.
gmap-2024-11-20/src/dynprog_genome.c:2946:49: style: Redundant pointer operation on 'bestrL' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2946:60: style: Redundant pointer operation on 'bestrR' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2946:71: style: Redundant pointer operation on 'bestcL' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2946:82: style: Redundant pointer operation on 'bestcR' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2946:93: style: Redundant pointer operation on 'best_introntype' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2953:47: style: Redundant pointer operation on 'bestrL' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2953:58: style: Redundant pointer operation on 'bestrR' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2953:69: style: Redundant pointer operation on 'bestcL' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2953:80: style: Redundant pointer operation on 'bestcR' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2986:26: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:2986:40: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3171:26: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3171:40: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3480:34: style: Redundant pointer operation on 'introntype' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3480:49: style: Redundant pointer operation on 'new_leftgenomepos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3480:71: style: Redundant pointer operation on 'new_rightgenomepos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3481:6: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3481:20: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3481:35: style: Redundant pointer operation on 'exonhead' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3482:6: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3482:26: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3482:39: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3818:11: style: Redundant pointer operation on 'introntype' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3818:26: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3818:40: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3842:40: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3842:60: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3842:73: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3842:89: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3842:100: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3871:41: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3871:61: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3871:74: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3871:90: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:3871:101: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/dynprog_genome.c:334:14: style: Parameter 'left_known' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:334:31: style: Parameter 'right_known' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2370:10: style: Parameter 'left_known' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2370:27: style: Parameter 'right_known' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2472:16: style: Parameter 'gsequenceL' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2472:34: style: Parameter 'gsequenceL_alt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2472:56: style: Parameter 'rev_gsequenceR' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2472:78: style: Parameter 'rev_gsequenceR_alt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2473:47: style: Parameter 'left_known' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2473:64: style: Parameter 'right_known' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:2491:8: style: Variable 'intron_score_array' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/dynprog_genome.c:3009:12: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3009:29: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3009:48: style: Parameter 'rev_rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3009:69: style: Parameter 'rev_rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3010:12: style: Parameter 'gsequenceL' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3010:30: style: Parameter 'gsequenceL_alt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3010:52: style: Parameter 'rev_gsequenceR' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3010:74: style: Parameter 'rev_gsequenceR_alt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/dynprog_genome.c:3030:8: style: Variable 'intron_score_array' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/dynprog_genome.c:3409:29: style: Variable 'rev_roffset' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/dynprog_genome.c:3427:29: style: Variable 'rev_roffset' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/dynprog_genome.c:3817:19: style: Variable 'finalscore' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/exon.c:65:28: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/exon.c:79:22: style: Redundant pointer operation on 'exons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/filestring.c:259:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/filestring.c:413:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/filestring.c:137:9: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/fopen.c:23:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/fopen.c:13:24: style: Parameter 'read_files_command' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/fopen.c:13:50: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome-write.c:57:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome-write.c:263:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome-write.c:396:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome-write.c:575:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome-write.c:624:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome-write.c:776:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome-write.c:321:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/genome-write.c:324:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/genome-write.c:704:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/genome-write.c:707:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/genome-write.c:207:45: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome-write.c:219:51: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome-write.c:220:8: style: Variable 'complCode' can be declared as const array [constVariable]
gmap-2024-11-20/src/genome-write.c:235:35: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome-write.c:375:38: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome-write.c:377:50: style: Variable 'segment' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genome-write.c:766:28: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/extension-search.c:2419:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/extension-search.c:2434:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/extension-search.c:298:22: style: Redundant pointer operation on 'set' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/extension-search.c:2029:18: style: Redundant pointer operation on 'univdiagonals_list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/extension-search.c:2029:41: style: Redundant pointer operation on 'auxinfo_list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/extension-search.c:2131:18: style: Redundant pointer operation on 'univdiagonals_list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/extension-search.c:2131:41: style: Redundant pointer operation on 'auxinfo_list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/extension-search.c:2231:18: style: Redundant pointer operation on 'univdiagonals_list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/extension-search.c:2231:41: style: Redundant pointer operation on 'auxinfo_list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/extension-search.c:180:32: style:inconclusive: Function 'Extension_search_setup' argument 1 names different: declaration 'mode' definition 'mode_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/extension-search.h:54:32: note: Function 'Extension_search_setup' argument 1 names different: declaration 'mode' definition 'mode_in'.
gmap-2024-11-20/src/extension-search.c:180:32: note: Function 'Extension_search_setup' argument 1 names different: declaration 'mode' definition 'mode_in'.
gmap-2024-11-20/src/extension-search.c:183:14: style:inconclusive: Function 'Extension_search_setup' argument 8 names different: declaration 'indexdb_fwd_in' definition 'indexdb_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/extension-search.h:57:14: note: Function 'Extension_search_setup' argument 8 names different: declaration 'indexdb_fwd_in' definition 'indexdb_in'.
gmap-2024-11-20/src/extension-search.c:183:14: note: Function 'Extension_search_setup' argument 8 names different: declaration 'indexdb_fwd_in' definition 'indexdb_in'.
gmap-2024-11-20/src/extension-search.c:183:36: style:inconclusive: Function 'Extension_search_setup' argument 9 names different: declaration 'indexdb_rev_in' definition 'indexdb_nonstd_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/extension-search.h:57:40: note: Function 'Extension_search_setup' argument 9 names different: declaration 'indexdb_rev_in' definition 'indexdb_nonstd_in'.
gmap-2024-11-20/src/extension-search.c:183:36: note: Function 'Extension_search_setup' argument 9 names different: declaration 'indexdb_rev_in' definition 'indexdb_nonstd_in'.
gmap-2024-11-20/src/extension-search.c:381:13: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/extension-search.c:528:13: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_canonical.c:80:84: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_canonical.c:139:88: style: Parameter 'ref_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_canonical.c:139:111: style: Parameter 'alt_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_canonical.c:219:32: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genome_sites.c:585:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome_sites.c:230:84: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_sites.c:290:88: style: Parameter 'ref_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_sites.c:290:111: style: Parameter 'alt_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_sites.c:366:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genome_sites.c:533:73: style: Parameter 'old_knownpos' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_sites.c:533:92: style: Parameter 'old_knowni' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome_sites.c:713:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits.c:220:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genome.c:245:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits.c:159:23: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.c:159:43: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.c:159:59: style: Parameter 'alt_suffix' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.c:164:7: style: Unused variable: npages0 [unusedVariable]
gmap-2024-11-20/src/genomebits.c:164:16: style: Unused variable: npages1 [unusedVariable]
gmap-2024-11-20/src/genomebits.c:164:25: style: Unused variable: npages2 [unusedVariable]
gmap-2024-11-20/src/genomebits_consec.c:696:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits_count.c:913:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits_consec.c:311:38: style:inconclusive: Function 'Genomebits_consecutive_matches_rightward' argument 4 names different: declaration 'left' definition 'querylength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/genomebits_consec.h:19:38: note: Function 'Genomebits_consecutive_matches_rightward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2024-11-20/src/genomebits_consec.c:311:38: note: Function 'Genomebits_consecutive_matches_rightward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2024-11-20/src/genomebits_consec.c:487:37: style:inconclusive: Function 'Genomebits_consecutive_matches_leftward' argument 4 names different: declaration 'left' definition 'querylength'. [funcArgNamesDifferent]
gmap-2024-11-20/src/genomebits_consec.h:23:37: note: Function 'Genomebits_consecutive_matches_leftward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2024-11-20/src/genomebits_consec.c:487:37: note: Function 'Genomebits_consecutive_matches_leftward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2024-11-20/src/genomebits_consec.c:56:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_consec.c:317:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genome.c:9015:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9016:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9017:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9018:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9027:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9042:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9043:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9044:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9045:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9054:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9070:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9071:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9072:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9073:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9098:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9099:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9100:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9101:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9110:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9146:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9147:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9148:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9149:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9158:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9169:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9170:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9171:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9172:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9181:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9193:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9194:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9195:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9196:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9217:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9218:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9219:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9220:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9229:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9447:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9448:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9449:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9450:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9468:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9479:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9480:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9481:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9482:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9500:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9512:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9513:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9514:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9515:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9546:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9547:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9548:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9549:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:9567:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genome.c:11080:17: style:inconclusive: Function 'Genome_get_segment_left' argument 5 names different: declaration 'left' definition 'right'. [funcArgNamesDifferent]
gmap-2024-11-20/src/genome.h:133:17: note: Function 'Genome_get_segment_left' argument 5 names different: declaration 'left' definition 'right'.
gmap-2024-11-20/src/genome.c:11080:17: note: Function 'Genome_get_segment_left' argument 5 names different: declaration 'left' definition 'right'.
gmap-2024-11-20/src/genome.c:208:19: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:208:39: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:208:55: style: Parameter 'alt_suffix' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:309:9: style: Variable 'accession' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genome.c:8868:57: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:8985:48: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:9120:57: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:9724:36: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:9767:49: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:11132:23: style: Parameter 'buffer1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:11132:38: style: Parameter 'buffer2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genome.c:10749:25: warning: Uninitialized variable: inbounds_low [uninitvar]
gmap-2024-11-20/src/genome.c:10733:41: note: Assuming condition is false
gmap-2024-11-20/src/genome.c:10749:25: note: Uninitialized variable: inbounds_low
gmap-2024-11-20/src/genome.c:213:7: style: Unused variable: npages [unusedVariable]
gmap-2024-11-20/src/genome.c:8992:17: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9127:17: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9457:9: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9464:10: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9489:9: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9496:10: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9523:11: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9530:12: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9556:11: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genome.c:9563:12: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_indel.c:2425:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits_count.c:826:28: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_count.c:840:28: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_count.c:848:28: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_count.c:857:33: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_count.c:868:27: style:inconclusive: Function 'Genomebits_count_setup' argument 1 names different: declaration 'ref' definition 'ref_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/genomebits_count.h:25:27: note: Function 'Genomebits_count_setup' argument 1 names different: declaration 'ref' definition 'ref_in'.
gmap-2024-11-20/src/genomebits_count.c:868:27: note: Function 'Genomebits_count_setup' argument 1 names different: declaration 'ref' definition 'ref_in'.
gmap-2024-11-20/src/genomebits_count.c:868:37: style:inconclusive: Function 'Genomebits_count_setup' argument 2 names different: declaration 'alt' definition 'alt_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/genomebits_count.h:25:34: note: Function 'Genomebits_count_setup' argument 2 names different: declaration 'alt' definition 'alt_in'.
gmap-2024-11-20/src/genomebits_count.c:868:37: note: Function 'Genomebits_count_setup' argument 2 names different: declaration 'alt' definition 'alt_in'.
gmap-2024-11-20/src/genomebits_count.c:61:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_count.c:196:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_count.c:379:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_count.c:607:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:883:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:883:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:883:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:883:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:883:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:883:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:48: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:82: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:20: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:55: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:20: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:47: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:20: style: Parameter 'snp_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:48: style: Parameter 'snp_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:75: style: Parameter 'snp_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:921:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:46: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:918:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:80: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:918:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:25: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:918:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:60: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:918:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:25: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:918:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:52: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:918:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:549:25: style: Parameter 'mask_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'mask_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_count.c:918:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits_count.c:57:19: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_count.c:192:19: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_kmer.c:445:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits_mismatches.c:1028:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits_kmer.c:40:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits_kmer.c:184:15: style: Variable 'diff_64' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_kmer.c:199:15: style: Variable 'diff_32' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_mismatches.c:464:39: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:469:43: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:503:39: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:508:43: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:930:40: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:934:44: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:968:40: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:973:44: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_mismatches.c:67:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_mismatches.c:257:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:998:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:998:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:998:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:998:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:998:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:998:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:48: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:82: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:20: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:55: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:20: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:47: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:20: style: Parameter 'snp_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:48: style: Parameter 'snp_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:75: style: Parameter 'snp_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1036:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:46: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1033:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:80: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1033:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:25: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1033:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:60: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1033:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:25: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1033:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:52: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1033:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:549:25: style: Parameter 'mask_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'mask_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_mismatches.c:1033:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomicpos.c:58:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/genomicpos.c:35:15: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_trim.c:939:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits_indel.c:1678:32: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:1678:49: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:1686:32: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:1686:49: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:1696:38: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:1703:31: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:2346:31: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:2346:48: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:2353:31: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:2353:48: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:2363:37: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:2370:30: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/genomebits_indel.c:544:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:544:7: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:544:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:544:25: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:794:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:794:7: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:794:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:794:25: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1102:8: style: Local variable 'query_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:45:13: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1102:8: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1103:8: style: Local variable 'genome_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:46:13: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1103:8: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1345:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1345:7: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1345:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1345:25: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1737:8: style: Local variable 'query_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:45:13: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1737:8: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1738:8: style: Local variable 'genome_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:46:13: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1738:8: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1986:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1986:7: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:1986:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2024-11-20/src/genomebits_indel.c:1986:25: note: Shadow variable
gmap-2024-11-20/src/genomebits_indel.c:365:54: style: Parameter 'query_high_blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits_indel.c:366:18: style: Parameter 'query_low_blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits_indel.c:366:50: style: Parameter 'query_flags_blocks' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits_indel.c:435:17: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_indel.c:1094:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits_indel.c:1258:44: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits_indel.c:1259:10: style: Parameter 'nmatches_baseline' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits_indel.c:1897:46: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits_indel.c:1898:12: style: Parameter 'nmatches_baseline' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2395:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2395:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2395:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2395:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2395:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2395:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:48: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:82: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:20: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:55: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:20: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:47: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:20: style: Parameter 'snp_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:48: style: Parameter 'snp_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:75: style: Parameter 'snp_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2433:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:46: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2430:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:80: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2430:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:25: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2430:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:60: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2430:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:25: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2430:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:52: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2430:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:549:25: style: Parameter 'mask_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'mask_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_indel.c:2430:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits_indel.c:432:19: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/getline.c:49:14: style: Variable 'length' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/get-genome.c:150:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:161:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:506:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:605:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:654:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:713:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:787:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:844:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:971:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/genomebits_trim.c:65:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:909:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:909:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:909:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:909:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:909:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:909:21: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:48: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:460:82: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:20: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:461:55: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:20: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:462:47: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:20: style: Parameter 'snp_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:48: style: Parameter 'snp_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:463:75: style: Parameter 'snp_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_wildcard_32' is a callback function, if 'snp_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:947:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:46: style: Parameter 'query_high_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_high_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:944:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:545:80: style: Parameter 'query_low_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_low_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:944:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:25: style: Parameter 'query_flags_shifted' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'query_flags_shifted' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:944:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:546:60: style: Parameter 'ref_high_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_high_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:944:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:25: style: Parameter 'ref_low_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_low_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:944:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:547:52: style: Parameter 'ref_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'ref_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:944:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits.h:549:25: style: Parameter 'mask_flags_ptr' can be declared as pointer to const. However it seems that 'block_diff_standard_masked_32' is a callback function, if 'mask_flags_ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
gmap-2024-11-20/src/genomebits_trim.c:944:25: note: You might need to cast the function pointer here
gmap-2024-11-20/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2024-11-20/src/genomebits_trim.c:174:8: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_trim.c:243:8: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_trim.c:389:10: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_trim.c:456:10: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_trim.c:603:8: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_trim.c:672:8: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_trim.c:818:10: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/genomebits_trim.c:886:10: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmap_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/gmap_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gmap_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gmap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gmap_select.c:43:5: note: Null pointer dereference
gmap-2024-11-20/src/gmap_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gmap_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gmap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gmap_select.c:45:3: note: Null pointer dereference
gmap-2024-11-20/src/gmap_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmap.c:685:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:893:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:4783:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:5059:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:5085:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:5122:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:5167:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:5236:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:5281:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:6069:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:6166:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:6790:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:399:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:426:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:468:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:700:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:888:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:1072:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:1316:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapindex.c:1415:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/get-genome.c:1827:11: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/get-genome.c:868:25: style: The comparison 'annotationonlyp == 0' is always true. [knownConditionTrueFalse]
gmap-2024-11-20/src/get-genome.c:818:26: note: 'annotationonlyp' is assigned value '0' here.
gmap-2024-11-20/src/get-genome.c:868:25: note: The comparison 'annotationonlyp == 0' is always true.
gmap-2024-11-20/src/get-genome.c:514:40: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:516:32: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:519:24: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:519:39: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:519:55: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:519:71: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:526:40: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:528:32: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:531:24: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:531:39: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:531:55: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:531:71: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:539:40: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:542:38: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:545:30: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:545:45: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:545:61: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:545:77: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/get-genome.c:769:16: style: Local variable 'uniquep' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/get-genome.c:79:13: note: Shadowed declaration
gmap-2024-11-20/src/get-genome.c:769:16: note: Shadow variable
gmap-2024-11-20/src/get-genome.c:246:37: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/get-genome.c:590:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/get-genome.c:636:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/get-genome.c:696:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/get-genome.c:767:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/get-genome.c:937:47: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmapl_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmapl_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/gmapl_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gmapl_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gmapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gmapl_select.c:43:5: note: Null pointer dereference
gmap-2024-11-20/src/gmapl_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gmapl_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gmapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gmapl_select.c:45:3: note: Null pointer dereference
gmap-2024-11-20/src/gmapl_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmapindex.c:409:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/gmapindex.c:487:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/gmapindex.c:1406:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/gmapindex.c:1408:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/gmapindex.c:2160:24: style: Comparing expression of type 'unsigned int' against value 4294967295. Condition is always false. [compareValueOutOfTypeRangeError]
gmap-2024-11-20/src/gmapindex.c:2224:24: style: Comparing expression of type 'unsigned int' against value 4294967295. Condition is always false. [compareValueOutOfTypeRangeError]
gmap-2024-11-20/src/gmapindex.c:475:12: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/gmapindex.c:1535:11: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/gmapindex.c:1539:22: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/gmapindex.c:1225:18: style: Redundant pointer operation on 'chrlength_table' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmapindex.c:1255:14: style: Redundant pointer operation on 'accsegmentpos_table' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmapindex.c:1280:14: style: Redundant pointer operation on 'alt_scaffold_info_table' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmapindex.c:456:15: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:683:30: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:683:50: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:864:32: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:864:52: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:1024:26: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:1024:46: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:1305:29: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gmapindex.c:1355:25: style: Variable 'source_dbroot' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmapindex.c:924:22: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmapindex.c:1233:12: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmapindex.c:1261:12: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/gsnap_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gsnap_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gsnap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gsnap_select.c:43:5: note: Null pointer dereference
gmap-2024-11-20/src/gsnap_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gsnap_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gsnap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gsnap_select.c:45:3: note: Null pointer dereference
gmap-2024-11-20/src/gsnap_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gsnapl_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:774:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:977:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:1775:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:2224:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:2288:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:2333:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:2403:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:2445:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:3397:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:3570:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:3596:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:3720:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:4162:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:4375:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:4897:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnapl_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/gsnapl_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gsnapl_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gsnapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gsnapl_select.c:43:5: note: Null pointer dereference
gmap-2024-11-20/src/gsnapl_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2024-11-20/src/gsnapl_select.c:41:30: note: Assuming allocation function fails
gmap-2024-11-20/src/gsnapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2024-11-20/src/gsnapl_select.c:45:3: note: Null pointer dereference
gmap-2024-11-20/src/gsnapl_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read-univ.c:302:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:976:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:992:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:1127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:1282:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:1440:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:1567:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:1847:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read-univ.c:1441:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1445:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1479:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1482:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1486:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1492:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1495:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1499:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read-univ.c:1686:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:1686:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:1706:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:1706:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2025:30: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2025:53: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2134:28: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2134:42: style: Redundant pointer operation on 'chrhigh' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2134:54: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2181:42: style: Redundant pointer operation on 'troffset' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2181:55: style: Redundant pointer operation on 'trhigh' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:2181:66: style: Redundant pointer operation on 'trlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read-univ.c:556:33: style: Parameter 'typestring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:654:17: style: Variable 'annotation' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read-univ.c:745:44: style: Parameter 'sam_read_group_id' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:745:69: style: Parameter 'sam_read_group_name' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:746:12: style: Parameter 'sam_read_group_library' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:746:42: style: Parameter 'sam_read_group_platform' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:815:9: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read-univ.c:986:65: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:1091:70: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:1729:45: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:1811:37: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read-univ.c:1813:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read-univ.c:997:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read-univ.c:1009:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read-univ.c:2160:19: style: Variable 'inbounds' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read-univ.c:2206:19: style: Variable 'inbounds' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read.c:128:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:1541:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:1561:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:1665:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:1807:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:1889:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable low [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:2304:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:2574:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:2812:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:3086:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:3509:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:4156:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:5221:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:5301:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:5385:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:5474:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:6629:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:6676:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:6720:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:6801:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:6894:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:6994:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:7096:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:7259:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gmap.c:5044:14: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/gmap.c:5050:21: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/gmap.c:5095:7: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
gmap-2024-11-20/src/gmap.c:6674:3: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/gmap.c:6848:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/gmap.c:6924:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/gmap.c:7119:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/gmap.c:4797:5: style: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/gmap.c:1464:34: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1464:53: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1464:71: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1464:87: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1610:34: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1610:53: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1610:71: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1610:87: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:1796:18: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2058:32: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2058:46: style: Redundant pointer operation on 'chrhigh' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2058:58: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2078:32: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2078:46: style: Redundant pointer operation on 'chrhigh' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2078:58: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2627:46: style: Redundant pointer operation on 'chimeraequivpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2628:11: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2628:22: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2628:33: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2628:47: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2655:12: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2655:23: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2655:34: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2655:48: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2656:18: style: Redundant pointer operation on 'donor_watsonp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2656:36: style: Redundant pointer operation on 'acceptor_watsonp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2656:57: style: Redundant pointer operation on 'donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:2656:72: style: Redundant pointer operation on 'acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:4213:31: style: Redundant pointer operation on 'mergedp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:4320:33: style: Redundant pointer operation on 'mergedp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:4320:45: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:4454:43: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:4472:20: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:4648:37: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:5084:21: style: Redundant pointer operation on 'part_modulus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:5095:21: style: Redundant pointer operation on 'part_interval' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gmap.c:6052:14: style: Local variable 'inbuffer' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/gmap.c:505:19: note: Shadowed declaration
gmap-2024-11-20/src/gmap.c:6052:14: note: Shadow variable
gmap-2024-11-20/src/gmap.c:5038:9: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmap.c:5038:31: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmap.c:5082:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmap.c:5115:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmap.c:5156:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmap.c:5218:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gmap.c:818:18: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmap.c:818:30: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmap.c:818:16: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmap.c:818:28: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmap.c:1511:22: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gmap.c:6118:16: style: Variable 'nextchar' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-write-univ.c:458:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write-univ.c:488:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write-univ.c:637:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write-univ.c:274:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/iit-write-univ.c:315:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/iit-write-univ.c:239:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write-univ.c:240:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write-univ.c:252:27: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write-univ.c:253:28: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write-univ.c:75:62: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:101:15: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2024-11-20/src/iit-write-univ.c:113:36: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:113:49: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:113:80: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:130:55: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:130:68: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:131:32: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:160:12: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:379:22: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write-univ.c:380:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write-univ.c:484:21: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write-univ.c:484:34: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write-univ.c:484:42: style: Variable 'annot' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write-univ.c:625:23: style: Parameter 'iitfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write-univ.c:119:10: style: Variable 'iota' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap.c:2234:7: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
gmap-2024-11-20/src/gsnap.c:4658:5: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/gsnap.c:4859:5: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/gsnap.c:4862:5: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/gsnap.c:4948:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/gsnap.c:5182:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/gsnap.c:5293:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/gsnap.c:1807:5: style: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/gsnap.c:1329:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1329:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1329:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1360:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1360:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1360:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1380:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1380:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1380:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1411:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1411:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1411:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1447:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1447:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1447:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1556:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1556:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:1556:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:2223:21: style: Redundant pointer operation on 'part_modulus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:2234:21: style: Redundant pointer operation on 'part_interval' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:3413:40: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:3426:35: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:3476:37: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:3536:43: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:3608:37: style: Redundant pointer operation on 'any_circular_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/gsnap.c:3383:8: style: Local variable 'fastq_format_p' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/gsnap.c:294:13: note: Shadowed declaration
gmap-2024-11-20/src/gsnap.c:3383:8: note: Shadow variable
gmap-2024-11-20/src/gsnap.c:3561:14: style: Local variable 'transcript_iit' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/gsnap.c:229:19: note: Shadowed declaration
gmap-2024-11-20/src/gsnap.c:3561:14: note: Shadow variable
gmap-2024-11-20/src/gsnap.c:3586:14: style: Local variable 'chromosome_iit' shadows outer variable [shadowVariable]
gmap-2024-11-20/src/gsnap.c:238:19: note: Shadowed declaration
gmap-2024-11-20/src/gsnap.c:3586:14: note: Shadow variable
gmap-2024-11-20/src/gsnap.c:2221:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gsnap.c:2281:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gsnap.c:2322:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gsnap.c:2385:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/gsnap.c:3560:15: style: Parameter 'transcriptomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gsnap.c:3560:42: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gsnap.c:3585:55: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gsnap.c:3585:75: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/gsnap.c:4324:22: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:576:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write.c:898:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write.c:1225:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable low [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write.c:1479:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write.c:1590:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/gsnap.c:1827:15: style: Modulo of one is always equal to zero [moduloofone]
gmap-2024-11-20/src/gsnap.c:900:18: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap.c:900:30: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap.c:900:16: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap.c:900:28: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap.c:1695:26: style: Variable 'max_localdb_nregions' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap.c:1696:24: style: Variable 'max_nintersections' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/gsnap.c:4337:12: style: Unused variable: worker_id [unusedVariable]
gmap-2024-11-20/src/iit_dump.c:48:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_dump.c:59:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_dump.c:172:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_dump.c:227:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-write.c:287:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/iit-write.c:326:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/iit-write.c:676:15: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2024-11-20/src/iit-write.c:670:15: note: First condition
gmap-2024-11-20/src/iit-write.c:676:15: note: Second condition
gmap-2024-11-20/src/iit-write.c:680:15: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2024-11-20/src/iit-write.c:676:15: note: First condition
gmap-2024-11-20/src/iit-write.c:680:15: note: Second condition
gmap-2024-11-20/src/iit-write.c:252:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write.c:253:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write.c:265:27: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write.c:266:28: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write.c:354:21: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write.c:583:27: style: Redundant pointer operation on 'i' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write.c:584:27: style: Redundant pointer operation on 'i' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-write.c:85:59: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:111:15: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2024-11-20/src/iit-write.c:123:36: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:123:49: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:123:76: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:140:55: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:140:68: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:141:28: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:170:12: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:427:23: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:428:23: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:441:58: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:485:22: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:486:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:492:58: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:626:14: style: Parameter 'nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:626:31: style: Parameter 'nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:626:44: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:626:65: style: Parameter 'cum_nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:633:9: style: Variable 'divstring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:717:15: style: Parameter 'nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:717:32: style: Parameter 'nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:717:45: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:717:66: style: Parameter 'cum_nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:722:9: style: Variable 'divstring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:794:48: style: Parameter 'alphas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:794:61: style: Parameter 'betas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:794:73: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:794:86: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:844:57: style: Parameter 'alphas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:844:70: style: Parameter 'betas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:844:82: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:844:95: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:894:21: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:894:34: style: Variable 'fieldstring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:894:48: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:894:56: style: Variable 'annot' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:1208:21: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:1208:34: style: Variable 'fieldstring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:1208:48: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-write.c:1466:18: style: Parameter 'iitfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-write.c:129:10: style: Variable 'iota' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-write.c:631:17: style: Variable 'pointer' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit_dump.c:103:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_store.c:89:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:100:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:297:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:459:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:523:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:605:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:778:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:861:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:966:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:91:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:102:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:288:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:353:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:460:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:717:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:816:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:883:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_get.c:998:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit_store.c:243:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_store.c:244:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:245:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:250:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_store.c:251:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:252:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:267:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_store.c:269:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:270:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:323:15: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_store.c:331:9: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:347:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:492:13: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/iit_store.c:749:32: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:750:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:769:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:777:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/iit_store.c:786:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/iit_store.c:794:13: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/iit_store.c:689:7: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/iit_store.c:296:7: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/iit_store.c:305:29: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/iit_store.c:380:29: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/iit_store.c:454:14: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/iit_store.c:563:5: warning: If memory allocation fails, then there is a possible null pointer dereference: header [nullPointerOutOfMemory]
gmap-2024-11-20/src/iit_store.c:562:29: note: Assuming allocation function fails
gmap-2024-11-20/src/iit_store.c:562:14: note: Assignment 'header=(char*)malloc((line_length+2)*sizeof(char))', assigned value is 0
gmap-2024-11-20/src/iit_store.c:563:5: note: Null pointer dereference
gmap-2024-11-20/src/iit_store.c:246:25: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:246:61: style: Redundant pointer operation on 'end' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:253:20: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:271:25: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:271:61: style: Redundant pointer operation on 'end' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:358:24: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:361:22: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:361:32: style: Redundant pointer operation on 'end' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:569:35: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:569:58: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:576:53: style: Redundant pointer operation on 'divlist' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:576:65: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:577:25: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:641:32: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:642:5: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:648:50: style: Redundant pointer operation on 'divlist' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:648:62: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:649:9: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_store.c:218:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_store.c:235:54: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_store.c:288:77: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_store.c:519:9: style: Variable 'line' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_store.c:766:39: style: Parameter 'labelstr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_store.c:810:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_store.c:826:29: style: Variable 'chr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_store.c:826:35: style: Variable 'idptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_store.c:939:9: style: Variable 'inputfile' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_get.c:287:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_get.c:352:16: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_get.c:374:16: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_get.c:459:16: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/iit_get.c:1177:18: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/iit_get.c:1108:5: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/iit_get.c:1337:7: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/iit_get.c:1187:20: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2024-11-20/src/iit_get.c:646:16: style: Variable 'annotation' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/iit_get.c:641:16: note: annotation is assigned
gmap-2024-11-20/src/iit_get.c:646:16: note: annotation is overwritten
gmap-2024-11-20/src/iit_get.c:470:27: style: Redundant pointer operation on 'total' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:553:35: style: Redundant pointer operation on 'lastcoord' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:556:30: style: Redundant pointer operation on 'lastcoord' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:707:77: style: Redundant pointer operation on 'divstring' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:707:91: style: Redundant pointer operation on 'coordstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:707:106: style: Redundant pointer operation on 'coordend' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:731:24: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:755:35: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:757:20: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:760:19: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:760:34: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:760:50: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:760:66: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:782:35: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:784:26: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:788:25: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:788:40: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:788:56: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:788:72: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:807:77: style: Redundant pointer operation on 'divstring' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:807:91: style: Redundant pointer operation on 'coordstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:807:106: style: Redundant pointer operation on 'coordend' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:823:29: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:839:30: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:860:30: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:876:77: style: Redundant pointer operation on 'divstring' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:876:91: style: Redundant pointer operation on 'coordstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:876:106: style: Redundant pointer operation on 'coordend' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:896:36: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:898:37: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:898:52: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:898:68: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:898:84: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit_get.c:170:22: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_get.c:180:25: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_get.c:200:32: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_get.c:285:9: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_get.c:314:19: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_get.c:326:50: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_get.c:396:54: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit_get.c:658:17: style: Variable 'annotation' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit_get.c:776:16: style: Variable 'nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit_get.c:844:25: style: Variable 'typeint' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit_get.c:1113:26: style: Variable 'universalp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/inbuffer.c:264:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb-cat.c:93:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb-cat.c:147:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb-cat.c:651:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb-cat.c:929:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/iit-read.c:7129:34: style: Condition 'pos<=exonend' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/iit-read.c:7117:17: note: Assuming that condition 'pos>exonend' is not redundant
gmap-2024-11-20/src/iit-read.c:7129:34: note: Condition 'pos<=exonend' is always true
gmap-2024-11-20/src/iit-read.c:7182:34: style: Condition 'pos>=exonend' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/iit-read.c:7170:17: note: Assuming that condition 'pos<exonend' is not redundant
gmap-2024-11-20/src/iit-read.c:7182:34: note: Condition 'pos>=exonend' is always true
gmap-2024-11-20/src/iit-read.c:7292:34: style: Condition 'pos<=exonend' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/iit-read.c:7280:17: note: Assuming that condition 'pos>exonend' is not redundant
gmap-2024-11-20/src/iit-read.c:7292:34: note: Condition 'pos<=exonend' is always true
gmap-2024-11-20/src/iit-read.c:7345:34: style: Condition 'pos>=exonend' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/iit-read.c:7333:17: note: Assuming that condition 'pos<exonend' is not redundant
gmap-2024-11-20/src/iit-read.c:7345:34: note: Condition 'pos>=exonend' is always true
gmap-2024-11-20/src/iit-read.c:2580:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2592:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2596:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2604:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2608:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2613:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2617:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2625:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2633:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2640:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2644:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2654:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2657:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2661:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2671:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2674:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2678:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2685:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2691:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2694:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:2698:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3092:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3107:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3111:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3131:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3135:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3140:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3144:2: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3169:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3173:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3179:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3182:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3191:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3194:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3198:5: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3208:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3211:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3215:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3233:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3236:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3240:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3259:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3262:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3266:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3312:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3315:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/iit-read.c:3319:7: error: Resource leak: fp [resourceLeak]
gmap-2024-11-20/src/indel.c:354:45: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/indel.c:358:45: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/indel.c:647:45: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/indel.c:651:45: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read.c:1983:19: portability: Casting between char * and double * which have an incompatible binary data representation. [invalidPointerCast]
gmap-2024-11-20/src/iit-read.c:3773:15: style: The comparison 'divread == READ_ALL' is always true because 'divread' and 'READ_ALL' represent the same value. [knownConditionTrueFalse]
gmap-2024-11-20/src/iit-read.c:3480:23: note: 'divread' is assigned value 'READ_ALL' here.
gmap-2024-11-20/src/iit-read.c:3773:15: note: The comparison 'divread == READ_ALL' is always true because 'divread' and 'READ_ALL' represent the same value.
gmap-2024-11-20/src/iit-read.c:3910:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read.c:3910:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read.c:3929:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read.c:3929:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/iit-read.c:5961:30: style:inconclusive: Function 'IIT_get_exact_multiple' argument 1 names different: declaration 'nmatches' definition 'nexactmatches'. [funcArgNamesDifferent]
gmap-2024-11-20/src/iit-read.h:210:30: note: Function 'IIT_get_exact_multiple' argument 1 names different: declaration 'nmatches' definition 'nexactmatches'.
gmap-2024-11-20/src/iit-read.c:5961:30: note: Function 'IIT_get_exact_multiple' argument 1 names different: declaration 'nmatches' definition 'nexactmatches'.
gmap-2024-11-20/src/iit-read.c:107:23: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:341:27: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:406:28: style: Parameter 'typestring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:430:29: style: Parameter 'fieldstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:659:39: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:776:9: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:813:9: style: Variable 'labelptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:813:20: style: Variable 'annotptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:815:17: style: Variable 'annotation' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:1250:40: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:1551:61: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:1651:60: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:1791:87: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:1863:65: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:2542:40: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:2789:31: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:3040:33: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:3951:40: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:4105:32: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:4107:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:5459:75: style: Parameter 'types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:5834:9: style: Parameter 'types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:6494:9: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:6512:33: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:6582:49: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:6605:13: style: Parameter 'genes_chrnum_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:6607:24: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:6652:14: style: Parameter 'genes_chrnum_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:6654:24: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:6701:24: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:6771:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:6889:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:6978:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/iit-read.c:7212:64: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:7538:62: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/iit-read.c:1705:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read.c:1726:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read.c:2667:13: style: Variable 'nfields' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read.c:2732:12: style: Variable 'offset' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/iit-read.c:2748:12: style: Variable 'offset' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/indexdb-cat.c:822:25: style: Comparing expression of type 'unsigned int' against value 4294967295. Condition is always true. [compareValueOutOfTypeRangeError]
gmap-2024-11-20/src/indexdb-cat.c:823:5: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/indexdb-cat.c:827:5: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/indexdb-cat.c:901:3: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/indexdb-cat.c:901:3: warning: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/indexdb-cat.c:127:15: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb-cat.c:128:43: style: Parameter 'genome_univcoord' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb-cat.c:184:10: style: Variable 'indexdb' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/indexdb-cat.c:736:21: style: Variable 'ifilenames' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/indexdb-write.c:532:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb-write.c:1234:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb-write.c:1996:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb-write.c:2511:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-approx-indices-uint4.c:246:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-approx-indices-uint4.c:210:31: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-approx-indices-uint4.c:246:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-approx-indices-uint4.c:250:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-approx-indices-uint4.c:210:31: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-approx-indices-uint4.c:250:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/indexdb-write.c:787:3: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/indexdb-write.c:468:30: style: Parameter 'destdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb-write.c:474:58: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb-write.c:475:9: style: Variable 'uppercaseCode' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb-write.c:477:9: style: Variable 'filesuffix' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb-write.c:1921:54: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb-write.c:1923:9: style: Variable 'uppercaseCode' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb-write.c:2469:7: style: Unused variable: offsetsmeta_fd [unusedVariable]
gmap-2024-11-20/src/indexdb-write.c:2469:23: style: Unused variable: offsetsstrm_fd [unusedVariable]
gmap-2024-11-20/src/indexdb-write.c:2482:32: style: Unused variable: offsetsstrm_access [unusedVariable]
gmap-2024-11-20/src/indexdb.c:477:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:755:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:1253:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:1565:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:1704:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:1761:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:1842:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:2050:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/indexdb.c:2805:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mask [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-approx-indices-uint8.c:237:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-approx-indices-uint8.c:205:30: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-approx-indices-uint8.c:237:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-approx-indices-uint8.c:241:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-approx-indices-uint8.c:205:30: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-approx-indices-uint8.c:241:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-concordance-uint4.c:269:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-concordance-uint4.c:236:31: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-concordance-uint4.c:269:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-concordance-uint4.c:273:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-concordance-uint4.c:236:31: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-concordance-uint4.c:273:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-higher-large.c:146:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-higher-large.c:192:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-higher-large.c:234:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-higher-large.c:270:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-higher-large.c:158:20: style: Condition '1||B_value+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-higher-large.c:202:20: style: Condition '1||A_value+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-higher-large.c:243:18: style: Condition '1||B_value+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-higher-large.c:278:18: style: Condition '1||A_value+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-higher-large.c:132:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-higher-large.c:179:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-higher-large.c:223:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-higher-large.c:259:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-concordance-uint8.c:261:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-concordance-uint8.c:229:30: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-concordance-uint8.c:261:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-concordance-uint8.c:265:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-concordance-uint8.c:229:30: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-concordance-uint8.c:265:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-higher-small.c:198:8: style: Condition '1||(*A)+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-higher-small.c:204:8: style: Condition '1||(*B)+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-higher-small.c:243:13: style: Condition '1||(*A)+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-higher-small.c:249:13: style: Condition '1||(*B)+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-indices-small.c:131:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-indices2-large.c:289:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-indices2-large.c:331:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-indices-uint8.c:123:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-indices2-large.c:125:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-indices2-large.c:210:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-indices2-large.c:284:16: style: Variable 'initB' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-indices2-large.c:325:16: style: Variable 'initA' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-large.c:160:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-large.c:1716:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-large.c:91:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-indices2-small.c:130:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intersect-lower-large.c:146:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-lower-large.c:192:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-lower-large.c:234:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-lower-large.c:270:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-lower-large.c:158:20: style: Condition '1||B_value+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-lower-large.c:202:20: style: Condition '1||A_value+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-lower-large.c:243:18: style: Condition '1||B_value+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-lower-large.c:278:18: style: Condition '1||A_value+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-lower-large.c:132:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-lower-large.c:179:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-lower-large.c:223:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-lower-large.c:259:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-lower-small.c:198:8: style: Condition '1||(*A)+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-lower-small.c:204:8: style: Condition '1||(*B)+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-lower-small.c:245:13: style: Condition '1||(*A)+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-lower-small.c:252:13: style: Condition '1||(*B)+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/intersect-uint2.c:73:20: style: Parameter 'set1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intersect-small.c:1121:44: warning: Uninitialized variable: diagonals [uninitvar]
gmap-2024-11-20/src/intersect-small.c:1117:18: note: Assuming condition is true
gmap-2024-11-20/src/intersect-small.c:1121:44: note: Uninitialized variable: diagonals
gmap-2024-11-20/src/intersect-small.c:1129:44: error: Uninitialized variable: diagonals [legacyUninitvar]
gmap-2024-11-20/src/intersect-small.c:1141:28: error: Uninitialized variable: diagonals [legacyUninitvar]
gmap-2024-11-20/src/intersect-small.c:1149:28: error: Uninitialized variable: diagonals [legacyUninitvar]
gmap-2024-11-20/src/intersect-small.c:86:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/interval.c:232:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/interval.c:255:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/intersect-wdups-indices.c:228:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-wdups-indices.c:193:31: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-wdups-indices.c:228:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/intersect-wdups-indices.c:232:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2024-11-20/src/intersect-wdups-indices.c:193:31: note: 'initA' is assigned value 'A' here.
gmap-2024-11-20/src/intersect-wdups-indices.c:232:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2024-11-20/src/indexdb.c:486:19: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
gmap-2024-11-20/src/indexdb.c:911:19: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
gmap-2024-11-20/src/indexdb.c:2460:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/indexdb.c:2500:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/indexdb.c:755:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'Blocksize_T {aka unsigned int}'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/indexdb.c:790:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'Blocksize_T {aka unsigned int}'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/indexdb.c:935:4: portability: %ld in format string (no. 3) requires 'long' but the argument type is 'ptrdiff_t {aka signed int}'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/indexdb.c:541:4: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/indexdb.c:938:4: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/intlistpool.c:221:29: style:inconclusive: Function 'Intlistpool_push' argument 1 names different: declaration 'intlist' definition 'list'. [funcArgNamesDifferent]
gmap-2024-11-20/src/intlistpool.h:71:29: note: Function 'Intlistpool_push' argument 1 names different: declaration 'intlist' definition 'list'.
gmap-2024-11-20/src/intlistpool.c:221:29: note: Function 'Intlistpool_push' argument 1 names different: declaration 'intlist' definition 'list'.
gmap-2024-11-20/src/indexdb.c:436:37: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:436:53: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:436:75: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:443:55: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb.c:452:18: style: Variable 'entry' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb.c:708:36: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:708:52: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:708:74: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:728:45: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb.c:735:18: style: Variable 'entry' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb.c:1243:59: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:1243:81: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:1552:61: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:1553:9: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/indexdb.c:2771:9: style: Variable 'uppercaseCode' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb.c:2776:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/indexdb.c:379:18: style: Variable 'oligospace' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/intlist.c:407:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2024-11-20/src/intlist.c:402:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2024-11-20/src/intlist.c:404:20: note: Assuming condition is false
gmap-2024-11-20/src/intlist.c:407:10: note: Null pointer dereference
gmap-2024-11-20/src/intlist.c:428:3: warning: Possible null pointer dereference: last [nullPointer]
gmap-2024-11-20/src/intlist.c:422:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2024-11-20/src/intlist.c:424:20: note: Assuming condition is false
gmap-2024-11-20/src/intlist.c:428:3: note: Null pointer dereference
gmap-2024-11-20/src/intlist.c:450:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2024-11-20/src/intlist.c:445:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2024-11-20/src/intlist.c:447:26: note: Assuming condition is false
gmap-2024-11-20/src/intlist.c:450:10: note: Null pointer dereference
gmap-2024-11-20/src/intlist.c:363:26: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intlist.c:523:18: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/intlist.c:524:18: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/intlist.c:537:18: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/intlist.c:538:18: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/intlist.c:555:18: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/intlist.c:556:18: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/intlist.c:762:31: style: Parameter 'deletep' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/intlist.c:378:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2024-11-20/src/junction.c:383:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/junction.c:81:13: style: Condition '0&&this->splice_distance==0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/junction.c:114:28: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/junction.c:129:22: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownindels.c:121:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/knownindels.c:219:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/knownindels.c:278:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/knownindels.c:318:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/knownsplicing.c:457:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/knownsplicing.c:985:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/knownindels.c:169:22: style: Parameter 'raw_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/knownindels.c:169:58: style: Parameter 'raw_counts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/knownindels.c:253:22: warning: Uninitialized variable: allocp [uninitvar]
gmap-2024-11-20/src/knownindels.c:230:17: note: Assuming condition is false
gmap-2024-11-20/src/knownindels.c:253:22: note: Uninitialized variable: allocp
gmap-2024-11-20/src/kmer-search.c:292:49: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:295:50: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:640:35: style: Redundant pointer operation on '_univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:640:54: style: Redundant pointer operation on 'auxinfo' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:640:66: style: Redundant pointer operation on 'pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:777:35: style: Redundant pointer operation on '_univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:777:54: style: Redundant pointer operation on 'auxinfo' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:777:66: style: Redundant pointer operation on 'pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:854:25: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:854:50: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:854:68: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:865:26: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:865:52: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:865:71: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/kmer-search.c:195:28: style:inconclusive: Function 'Kmer_exact1' argument 10 names different: declaration 'querystart' definition 'kmer_querystart'. [funcArgNamesDifferent]
gmap-2024-11-20/src/kmer-search.h:47:28: note: Function 'Kmer_exact1' argument 10 names different: declaration 'querystart' definition 'kmer_querystart'.
gmap-2024-11-20/src/kmer-search.c:195:28: note: Function 'Kmer_exact1' argument 10 names different: declaration 'querystart' definition 'kmer_querystart'.
gmap-2024-11-20/src/kmer-search.c:195:49: style:inconclusive: Function 'Kmer_exact1' argument 11 names different: declaration 'queryend' definition 'kmer_queryend'. [funcArgNamesDifferent]
gmap-2024-11-20/src/kmer-search.h:47:44: note: Function 'Kmer_exact1' argument 11 names different: declaration 'queryend' definition 'kmer_queryend'.
gmap-2024-11-20/src/kmer-search.c:195:49: note: Function 'Kmer_exact1' argument 11 names different: declaration 'queryend' definition 'kmer_queryend'.
gmap-2024-11-20/src/list.c:443:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2024-11-20/src/list.c:438:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2024-11-20/src/list.c:440:20: note: Assuming condition is false
gmap-2024-11-20/src/list.c:443:10: note: Null pointer dereference
gmap-2024-11-20/src/list.c:191:18: style:inconclusive: Function 'List_head_set' argument 1 names different: declaration 'list' definition 'this'. [funcArgNamesDifferent]
gmap-2024-11-20/src/list.h:224:30: note: Function 'List_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2024-11-20/src/list.c:191:18: note: Function 'List_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2024-11-20/src/list.c:522:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/list.c:361:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2024-11-20/src/kmer-search.c:387:18: style: Parameter 'exhaustive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/kmer-search.c:387:35: style: Parameter 'qstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/kmer-search.c:387:49: style: Parameter 'qends' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/kmer-search.c:457:16: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:504:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/knownsplicing.c:641:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:641:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:668:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:668:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:695:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:695:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:722:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:722:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/knownsplicing.c:957:59: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/knownsplicing.c:1048:33: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/knownsplicing.c:1048:55: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/knownsplicing.c:1068:34: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/knownsplicing.c:1068:56: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/knownsplicing.c:285:18: style: Variable 'nintervals' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/knownsplicing.c:374:11: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/localdb-write.c:393:8: style: Variable 'kmer' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/localdb-write.c:364:8: note: kmer is assigned
gmap-2024-11-20/src/localdb-write.c:393:8: note: kmer is overwritten
gmap-2024-11-20/src/localdb-write.c:115:64: style: Parameter 'sarray16' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:116:11: style: Parameter 'gbuffer16' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:120:9: style: Variable 'oligo' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/localdb-write.c:168:62: style: Parameter 'saindex16' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:224:65: style: Parameter 'intstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:482:22: style: Parameter 'saindex16file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:482:43: style: Parameter 'sarray16file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:483:15: style: Parameter 'sarray8file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-write.c:483:34: style: Parameter 'sasort16file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/mapq.c:77:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mapq.c:165:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mapq.c:66:31: style: Parameter 'quality_string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/mapq.c:155:27: style: Parameter 'genomic_diff' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/mapq.c:155:47: style: Parameter 'quality_string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/match.c:175:32: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/match.c:176:9: style: Variable 'genomicseg_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/localdb-read.c:2548:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/localdb-read.c:1850:16: style: Condition 'nptrs5>0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/localdb-read.c:1827:19: note: Assuming that condition 'highi5>=lowi5' is not redundant
gmap-2024-11-20/src/localdb-read.c:1830:29: note: Assignment 'nptrs5=highi5-lowi5+1', assigned value is less than 1
gmap-2024-11-20/src/localdb-read.c:1850:16: note: Condition 'nptrs5>0' is always false
gmap-2024-11-20/src/localdb-read.c:972:25: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:1012:27: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:1725:24: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:1725:40: style: Redundant pointer operation on 'univdiags' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:2385:37: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:2385:53: style: Redundant pointer operation on 'univdiags_alloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:2399:28: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:2399:44: style: Redundant pointer operation on 'univdiags_alloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:2413:28: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:2413:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:2413:60: style: Redundant pointer operation on 'univdiags_alloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/localdb-read.c:200:78: style: Parameter 'SA' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:201:14: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:332:17: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:352:22: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:384:79: style: Parameter 'saindex' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:384:98: style: Parameter 'SA' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:1914:28: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/localdb-read.c:1964:34: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/localdb-read.c:2026:13: style: Variable 'saindex16' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/localdb-read.c:2027:13: style: Variable 'sasort16' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/localdb-read.c:2522:20: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:2522:40: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/localdb-read.c:206:16: style: Variable 'nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/localdb-read.c:390:16: style: Variable 'nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/localdb-read.c:2057:10: style: Variable 'trim5p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/localdb-read.c:2057:19: style: Variable 'trim3p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/md5.c:208:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/md5.c:221:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/maxent.c:98999:16: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99021:37: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99040:24: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99063:21: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99098:42: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99129:29: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99247:54: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99338:57: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/maxent.c:99353:22: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/md5.c:78:39: style: Parameter 'input' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/md5.c:93:39: style: Parameter 'input' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/mem.c:528:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:624:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:698:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:783:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:848:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:912:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:954:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:1046:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:1127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:1200:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:1275:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:1736:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/mem.c:953:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/mem.c:1045:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/mem.c:1126:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/mem.c:1199:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/mem.c:1274:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:173:23: style:inconclusive: Function 'Merge_diagonals' argument 1 names different: declaration 'nelts1' definition 'nelts'. [funcArgNamesDifferent]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.h:15:23: note: Function 'Merge_diagonals' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:173:23: note: Function 'Merge_diagonals' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:295:29: style:inconclusive: Function 'Merge_diagonals_uint4' argument 1 names different: declaration 'nelts1' definition 'nelts'. [funcArgNamesDifferent]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.h:21:29: note: Function 'Merge_diagonals_uint4' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:295:29: note: Function 'Merge_diagonals_uint4' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:121:35: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:122:13: style: Parameter 'diagterm_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:123:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:177:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:247:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:248:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint4.c:299:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:122:13: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:122:36: style: Parameter 'diagterm_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:123:18: style: Variable 'stream_high' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:124:10: style: Variable 'stream_low' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:180:18: style: Variable 'stream_high' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:181:10: style: Variable 'stream_low' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:251:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:252:16: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:303:16: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:149:17: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
gmap-2024-11-20/src/merge-diagonals-heap-uint8.c:201:15: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
gmap-2024-11-20/src/merge-diagonals-simd-uint4.c:127:13: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-simd-uint4.c:127:36: style: Parameter 'diagterm_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-simd-uint4.c:346:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-simd-uint4.c:413:11: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/merge-uint4.c:270:26: style: Variable 'Aend' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-uint4.c:270:33: style: Variable 'Bend' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-uint4.c:271:16: style: Unused variable: nextA [unusedVariable]
gmap-2024-11-20/src/merge-uint4.c:271:23: style: Unused variable: nextB [unusedVariable]
gmap-2024-11-20/src/merge-uint8.c:244:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/merge-diagonals-simd-uint8.c:328:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/merge-diagonals-simd-uint8.c:395:9: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/merge-uint8.c:227:19: style: Variable 'Aend' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-uint8.c:227:26: style: Variable 'Bend' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/merge-uint8.c:228:9: style: Unused variable: nextA [unusedVariable]
gmap-2024-11-20/src/merge-uint8.c:228:16: style: Unused variable: nextB [unusedVariable]
gmap-2024-11-20/src/method.c:12:20: style: Parameter 'methodp' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/nr-x.c:14:17: style: Variable 'cof' can be declared as const array [constVariable]
gmap-2024-11-20/src/oligo.c:504:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/oligo.c:224:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:224:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:224:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:226:38: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:226:51: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:226:63: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:232:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:232:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:232:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:356:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:356:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:356:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:358:38: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:358:51: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:358:63: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:364:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:364:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:364:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:378:35: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:378:48: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:378:60: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:381:33: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:381:46: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:381:58: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:399:35: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:399:48: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:399:60: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:402:33: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:402:46: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/oligo.c:402:58: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/orderstat.c:204:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/orderstat.c:218:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/orderstat.c:232:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/orderstat.c:246:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/orderstat.c:199:29: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/orderstat.c:213:23: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/orderstat.c:227:33: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/orderstat.c:241:33: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/outbuffer.c:194:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/outbuffer.c:1190:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/outbuffer.c:1334:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/outbuffer.c:1353:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/outbuffer.c:1334:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/outbuffer.c:1479:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/outbuffer.c:1495:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/outbuffer.c:1479:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/outbuffer.c:1160:60: style:inconclusive: Function 'Outbuffer_print_filestrings' argument 2 names different: declaration 'fp_failedinput_1' definition 'fp_failedinput'. [funcArgNamesDifferent]
gmap-2024-11-20/src/outbuffer.h:70:60: note: Function 'Outbuffer_print_filestrings' argument 2 names different: declaration 'fp_failedinput_1' definition 'fp_failedinput'.
gmap-2024-11-20/src/outbuffer.c:1160:60: note: Function 'Outbuffer_print_filestrings' argument 2 names different: declaration 'fp_failedinput_1' definition 'fp_failedinput'.
gmap-2024-11-20/src/outbuffer.c:149:25: style: Parameter 'failedinput_root' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:19339:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/oligoindex_hr.c:20506:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/oligoindex_hr.c:30838:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/oligoindex_hr.c:31818:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/output.c:913:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/output.c:85:57: style:inconclusive: Function 'Output_setup' argument 14 names different: declaration 'sam_flippedp' definition 'sam_flippedp_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/output.h:33:57: note: Function 'Output_setup' argument 14 names different: declaration 'sam_flippedp' definition 'sam_flippedp_in'.
gmap-2024-11-20/src/output.c:85:57: note: Function 'Output_setup' argument 14 names different: declaration 'sam_flippedp' definition 'sam_flippedp_in'.
gmap-2024-11-20/src/pair.c:1035:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:1145:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:1238:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:1477:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:1644:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:1711:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:1973:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:2013:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:2197:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:3004:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:3334:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:4026:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:4453:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:4707:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:4844:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:4867:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:5409:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:5713:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:5862:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:6046:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:6267:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:7837:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:7884:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:8014:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:8051:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:8132:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:8227:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:8380:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:8476:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:8622:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:9846:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pair.c:9999:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/oligoindex_hr.c:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
gmap-2024-11-20/src/oligoindex_hr.c:20695:7: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/oligoindex_hr.c:32001:7: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/oligoindex_hr.c:33877:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/oligoindex_hr.c:33912:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/oligoindex_hr.c:9108:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:9212:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:9316:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:9420:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:9524:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:9881:10: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/oligoindex_hr.c:11373:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:13115:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:14877:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:16661:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:18429:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:21411:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:21515:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:21618:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:21722:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:21825:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:22815:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:24589:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:26380:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:28164:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:29931:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:33075:22: style: Parameter 'inquery' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:33214:30: style: Parameter 'sumx' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:33214:41: style: Parameter 'sumxx' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:33294:45: style: Parameter 'sumx' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:33294:56: style: Parameter 'sumxx' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:33371:43: style: Parameter 'sumx' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:33371:54: style: Parameter 'sumxx' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:34127:50: style: Parameter 'coveredp' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/oligoindex_hr.c:9072:23: warning: Shifting 32-bit value by 4294967250 bits is undefined behaviour. See condition at line 9070. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9070:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9072:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9089:24: warning: Shifting 32-bit value by 4294967282 bits is undefined behaviour. See condition at line 9087. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9087:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9089:24: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9118:23: warning: Shifting 32-bit value by 4294967250 bits is undefined behaviour. See condition at line 9116. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:20560:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9116:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9118:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9176:23: warning: Shifting 32-bit value by 4294967248 bits is undefined behaviour. See condition at line 9174. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9174:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9176:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9193:24: warning: Shifting 32-bit value by 4294967280 bits is undefined behaviour. See condition at line 9191. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9191:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9193:24: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9222:23: warning: Shifting 32-bit value by 4294967248 bits is undefined behaviour. See condition at line 9220. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:20562:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9220:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9222:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9280:23: warning: Shifting 32-bit value by 4294967246 bits is undefined behaviour. See condition at line 9278. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9278:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9280:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9297:24: warning: Shifting 32-bit value by 4294967278 bits is undefined behaviour. See condition at line 9295. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9295:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9297:24: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9326:23: warning: Shifting 32-bit value by 4294967246 bits is undefined behaviour. See condition at line 9324. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:20564:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9324:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9326:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9384:23: warning: Shifting 32-bit value by 4294967244 bits is undefined behaviour. See condition at line 9382. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9382:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9384:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9401:24: warning: Shifting 32-bit value by 4294967276 bits is undefined behaviour. See condition at line 9399. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9399:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9401:24: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9430:23: warning: Shifting 32-bit value by 4294967244 bits is undefined behaviour. See condition at line 9428. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:20566:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9428:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9430:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9488:23: warning: Shifting 32-bit value by 4294967242 bits is undefined behaviour. See condition at line 9486. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9486:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9488:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9505:24: warning: Shifting 32-bit value by 4294967274 bits is undefined behaviour. See condition at line 9503. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9503:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9505:24: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9534:23: warning: Shifting 32-bit value by 4294967242 bits is undefined behaviour. See condition at line 9532. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:20568:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9532:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9534:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:21383:23: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 21381. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:30771:24: note: Assignment 'left_plus_length=0', assigned value is 0
gmap-2024-11-20/src/oligoindex_hr.c:30779:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
gmap-2024-11-20/src/oligoindex_hr.c:30828:77: note: Calling function 'count_9mers_rev_partial', 6th argument 'enddiscard' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:21381:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:21383:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:21400:26: warning: Shifting 32-bit value by 64 bits is undefined behaviour. See condition at line 21398. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:30771:24: note: Assignment 'left_plus_length=0', assigned value is 0
gmap-2024-11-20/src/oligoindex_hr.c:30779:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
gmap-2024-11-20/src/oligoindex_hr.c:30828:77: note: Calling function 'count_9mers_rev_partial', 6th argument 'enddiscard' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:21398:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:21400:26: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:21432:23: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 21430. [shiftTooManyBits]
gmap-2024-11-20/src/oligoindex_hr.c:31750:24: note: Assignment 'left_plus_length=0', assigned value is 0
gmap-2024-11-20/src/oligoindex_hr.c:31759:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
gmap-2024-11-20/src/oligoindex_hr.c:31808:109: note: Calling function 'store_9mers_rev_partial', 9th argument 'enddiscard' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:21430:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:21432:23: note: Shift
gmap-2024-11-20/src/oligoindex_hr.c:9072:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*9)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9070:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9072:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9089:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*9)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9087:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9089:34: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9118:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*9)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:20560:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9116:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9118:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9176:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*8)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9174:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9176:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9193:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*8)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9191:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9193:34: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9222:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*8)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:20562:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9220:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9222:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9280:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*7)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9278:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9280:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9297:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*7)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9295:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9297:34: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9326:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*7)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:20564:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9324:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9326:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9384:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*6)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9382:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9384:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9401:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*6)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9399:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9401:34: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9430:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*6)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:20566:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9428:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9430:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9488:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*5)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9486:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9488:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9505:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*5)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9503:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9505:34: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9534:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*5)'. [integerOverflowCond]
gmap-2024-11-20/src/oligoindex_hr.c:20568:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9532:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9534:33: note: Integer overflow
gmap-2024-11-20/src/oligoindex_hr.c:9072:33: warning: Expression '2*pos-(64-2*9)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9070:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9072:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9089:34: warning: Expression '2*pos-(32-2*9)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9087:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9089:34: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9118:33: warning: Expression '2*pos-(64-2*9)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:20560:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9116:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9118:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9176:33: warning: Expression '2*pos-(64-2*8)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9174:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9176:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9193:34: warning: Expression '2*pos-(32-2*8)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9191:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9193:34: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9222:33: warning: Expression '2*pos-(64-2*8)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:20562:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9220:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9222:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9280:33: warning: Expression '2*pos-(64-2*7)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9278:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9280:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9297:34: warning: Expression '2*pos-(32-2*7)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9295:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9297:34: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9326:33: warning: Expression '2*pos-(64-2*7)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:20564:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9324:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9326:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9384:33: warning: Expression '2*pos-(64-2*6)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9382:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9384:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9401:34: warning: Expression '2*pos-(32-2*6)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9399:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9401:34: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9430:33: warning: Expression '2*pos-(64-2*6)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:20566:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9428:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9430:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9488:33: warning: Expression '2*pos-(64-2*5)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9486:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9488:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9505:34: warning: Expression '2*pos-(32-2*5)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9503:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9505:34: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:9534:33: warning: Expression '2*pos-(64-2*5)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
gmap-2024-11-20/src/oligoindex_hr.c:20568:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
gmap-2024-11-20/src/oligoindex_hr.c:9532:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2024-11-20/src/oligoindex_hr.c:9534:33: note: Negative value is converted to an unsigned value
gmap-2024-11-20/src/oligoindex_hr.c:20496:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20498:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20500:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20502:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20504:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20687:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20689:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20691:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20693:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:20695:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31808:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31810:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31812:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31814:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31816:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31993:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31995:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31997:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:31999:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:32001:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/oligoindex_hr.c:33854:16: style: Unused variable: i [unusedVariable]
gmap-2024-11-20/src/pairpool.c:851:16: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
gmap-2024-11-20/src/pairpool.c:848:17: note: outer condition: path!=NULL
gmap-2024-11-20/src/pairpool.c:851:16: note: identical inner condition: path!=NULL
gmap-2024-11-20/src/pairpool.c:941:17: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
gmap-2024-11-20/src/pairpool.c:938:18: note: outer condition: pairs!=NULL
gmap-2024-11-20/src/pairpool.c:941:17: note: identical inner condition: pairs!=NULL
gmap-2024-11-20/src/pairpool.c:854:22: style: Condition 'end3_pairs!=NULL' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/pairpool.c:944:21: style: Condition 'end5_path!=NULL' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/pairpool.c:1044:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pairpool.c:679:37: style: Parameter 'source' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pairpool.c:981:69: style: Parameter 'querysequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pairpool.c:1069:11: style: Parameter 'genomesequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/parserange.c:187:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/parserange.c:258:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/parserange.c:306:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/parserange.c:435:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/parserange.c:600:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/parserange.c:710:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/parserange.c:84:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/parserange.c:85:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/parserange.c:86:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/parserange.c:103:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/parserange.c:104:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/parserange.c:105:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/parserange.c:122:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/parserange.c:124:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/parserange.c:125:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2024-11-20/src/parserange.c:296:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/parserange.c:387:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/parserange.c:559:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/parserange.c:691:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/parserange.c:310:23: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/parserange.c:412:16: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/parserange.c:578:16: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/parserange.c:709:16: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/parserange.c:108:60: style: Redundant pointer operation on 'length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:113:38: style: Redundant pointer operation on 'length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:264:46: style: Redundant pointer operation on 'chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:277:46: style: Redundant pointer operation on 'chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:332:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:354:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:414:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:414:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:418:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:418:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:419:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:422:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:422:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:495:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:517:30: style: Redundant pointer operation on 'chrstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:580:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:580:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:583:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:583:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:584:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:587:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:587:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:616:24: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:616:41: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:619:24: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:619:41: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:620:52: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:623:24: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:623:41: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:647:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:662:34: style: Redundant pointer operation on 'chrstart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:716:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/parserange.c:30:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/parserange.c:53:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/parserange.c:76:80: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/parserange.c:250:44: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/parserange.c:250:64: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/parserange.c:683:12: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path-eval.c:2223:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path-eval.c:852:35: style: Expression is always false because 'else if' condition matches previous condition at line 847. [multiCondition]
gmap-2024-11-20/src/path-eval.c:662:25: style: Condition 'qstart<chop_qend' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/path-eval.c:659:25: note: Assuming that condition 'qstart>=chop_qend' is not redundant
gmap-2024-11-20/src/path-eval.c:662:25: note: Condition 'qstart<chop_qend' is always true
gmap-2024-11-20/src/path-eval.c:748:25: style: Condition 'qstart<chop_qend' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/path-eval.c:745:25: note: Assuming that condition 'qstart>=chop_qend' is not redundant
gmap-2024-11-20/src/path-eval.c:748:25: note: Condition 'qstart<chop_qend' is always true
gmap-2024-11-20/src/path-eval.c:902:20: style: Condition 'qstart<chop_qend' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/path-eval.c:899:20: note: Assuming that condition 'qstart>=chop_qend' is not redundant
gmap-2024-11-20/src/path-eval.c:902:20: note: Condition 'qstart<chop_qend' is always true
gmap-2024-11-20/src/path-eval.c:1062:67: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path-eval.c:1063:45: style: Parameter 'queryrc' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path-eval.c:153:15: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:154:19: style: Variable 'ref_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:390:17: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:592:34: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:666:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:674:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:690:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:752:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:760:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:776:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:850:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:856:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:867:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:905:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:911:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:922:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:1135:16: style: Variable 'ninserts' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:1423:7: style: Unused variable: chop_qstart [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1423:20: style: Unused variable: chop_qend [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1424:7: style: Unused variable: chopped_nmatches_a [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1424:27: style: Unused variable: chopped_nmatches_b [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1659:6: style: Unused variable: coverage_a [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1659:18: style: Unused variable: coverage_b [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1670:7: style: Unused variable: chopped_nmatches_a [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1670:27: style: Unused variable: chopped_nmatches_b [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1670:47: style: Unused variable: chop_qstart [unusedVariable]
gmap-2024-11-20/src/path-eval.c:1670:60: style: Unused variable: chop_qend [unusedVariable]
gmap-2024-11-20/src/path-eval.c:2031:18: style: Variable 'junction_prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:2055:18: style: Variable 'junction_prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-eval.c:1793:30: style: Unused variable: prob [unusedVariable]
gmap-2024-11-20/src/path-eval.c:2919:21: style: Variable 'assignedp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-learn.c:246:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path-fusion.c:2121:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:2395:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:2671:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:2943:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:3185:13: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:3425:13: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:3679:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:3929:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:4182:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:4428:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-fusion.c:404:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/path-fusion.c:409:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/path-fusion.c:404:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/path-fusion.c:814:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/path-fusion.c:819:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/path-fusion.c:814:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/path-fusion.c:2120:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2121:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2394:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2395:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2670:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2671:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2942:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2943:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3184:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3185:49: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3195:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3424:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3425:49: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3435:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3574:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3652:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3678:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3679:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3824:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3902:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3928:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:3929:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4077:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4155:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4181:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4182:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4323:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4401:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4427:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:4428:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-fusion.c:2979:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/path-fusion.c:3223:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:6442:7: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2024-11-20/src/pair.c:9925:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2024-11-20/src/pair.c:473:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/pair.c:868:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/pair.c:881:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/pair.c:2739:31: style: Expression is always false because 'else if' condition matches previous condition at line 2737. [multiCondition]
gmap-2024-11-20/src/path-fusion.c:244:7: style: Unused variable: desired_genestrand [unusedVariable]
gmap-2024-11-20/src/path-fusion.c:245:8: style: Unused variable: extend_qstart_p [unusedVariable]
gmap-2024-11-20/src/path-fusion.c:245:25: style: Unused variable: extend_qend_p [unusedVariable]
gmap-2024-11-20/src/path-fusion.c:654:7: style: Unused variable: desired_genestrand [unusedVariable]
gmap-2024-11-20/src/path-fusion.c:655:8: style: Unused variable: extend_qstart_p [unusedVariable]
gmap-2024-11-20/src/path-fusion.c:655:25: style: Unused variable: extend_qend_p [unusedVariable]
gmap-2024-11-20/src/path-fusion.c:3488:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-fusion.c:3738:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-fusion.c:3989:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-fusion.c:4235:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:7810:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:7811:12: note: Assignment 'in_intron=1'
gmap-2024-11-20/src/pair.c:7810:11: note: Condition '!in_intron' is redundant
gmap-2024-11-20/src/pair.c:7814:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:7815:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:7814:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:7862:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:7863:12: note: Assignment 'in_intron=1'
gmap-2024-11-20/src/pair.c:7862:11: note: Condition '!in_intron' is redundant
gmap-2024-11-20/src/pair.c:7866:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:7867:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:7866:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:7996:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:7997:12: note: Assignment 'in_intron=1'
gmap-2024-11-20/src/pair.c:7996:11: note: Condition '!in_intron' is redundant
gmap-2024-11-20/src/pair.c:8000:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8001:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8000:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:8034:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8035:12: note: Assignment 'in_intron=1'
gmap-2024-11-20/src/pair.c:8034:11: note: Condition '!in_intron' is redundant
gmap-2024-11-20/src/pair.c:8038:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8039:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8038:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:8117:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8118:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8117:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:8212:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8213:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8212:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:8361:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8362:12: note: Assignment 'in_intron=1'
gmap-2024-11-20/src/pair.c:8361:11: note: Condition '!in_intron' is redundant
gmap-2024-11-20/src/pair.c:8365:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8366:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8365:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:8460:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8461:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8460:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:8656:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8657:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8656:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:8749:11: style: The statement 'if (in_exon) in_exon=0' is logically equivalent to 'in_exon=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8750:10: note: Assignment 'in_exon=0'
gmap-2024-11-20/src/pair.c:8749:11: note: Condition 'in_exon' is redundant
gmap-2024-11-20/src/pair.c:8775:11: style: The statement 'if (in_exon) in_exon=0' is logically equivalent to 'in_exon=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8776:10: note: Assignment 'in_exon=0'
gmap-2024-11-20/src/pair.c:8775:11: note: Condition 'in_exon' is redundant
gmap-2024-11-20/src/pair.c:8834:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:8835:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:8834:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:9543:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:9544:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:9543:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:9591:8: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:9592:16: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:9591:8: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:9657:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2024-11-20/src/pair.c:9658:12: note: Assignment 'in_intron=0'
gmap-2024-11-20/src/pair.c:9657:11: note: Condition 'in_intron' is redundant
gmap-2024-11-20/src/pair.c:2011:49: style: Condition 'this->querypos-prev_querypos>1' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/pair.c:2007:26: note: Assuming that condition 'this->querypos>prev_querypos' is not redundant
gmap-2024-11-20/src/pair.c:2011:49: note: Condition 'this->querypos-prev_querypos>1' is always false
gmap-2024-11-20/src/pair.c:8819:28: style: Condition 'cdna_direction==0' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/pair.c:8811:28: note: Assuming that condition 'cdna_direction<0' is not redundant
gmap-2024-11-20/src/pair.c:8803:21: note: Assuming that condition 'cdna_direction>0' is not redundant
gmap-2024-11-20/src/pair.c:8819:28: note: Condition 'cdna_direction==0' is always true
gmap-2024-11-20/src/pair.c:944:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/pair.c:946:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/pair.c:974:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/pair.c:976:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/pair.c:1585:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/pair.c:1671:5: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/pair.c:1711:5: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/pair.c:5373:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/pair.c:5669:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/pair.c:1149:7: style: Variable 'ptr' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/pair.c:1137:9: note: ptr is assigned
gmap-2024-11-20/src/pair.c:1149:7: note: ptr is overwritten
gmap-2024-11-20/src/pair.c:1149:7: style: Variable 'ptr' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/pair.c:1139:9: note: ptr is assigned
gmap-2024-11-20/src/pair.c:1149:7: note: ptr is overwritten
gmap-2024-11-20/src/pair.c:1970:2: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/pair.c:2010:2: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/pair.c:8626:7: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/pair.c:2390:17: style: Redundant pointer operation on 'tokens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pair.c:5834:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pair.c:5834:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pair.c:5834:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pair.c:5837:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pair.c:5837:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pair.c:5837:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pair.c:3669:100: style:inconclusive: Function 'Pair_print_gff3' argument 6 names different: declaration 'restofheader' definition 'fasta_annotation'. [funcArgNamesDifferent]
gmap-2024-11-20/src/pair.h:162:100: note: Function 'Pair_print_gff3' argument 6 names different: declaration 'restofheader' definition 'fasta_annotation'.
gmap-2024-11-20/src/pair.c:3669:100: note: Function 'Pair_print_gff3' argument 6 names different: declaration 'restofheader' definition 'fasta_annotation'.
gmap-2024-11-20/src/pair.c:3868:46: style:inconclusive: Function 'Pair_print_bedpe' argument 2 names different: declaration 'pairs_querydir' definition 'pairarray'. [funcArgNamesDifferent]
gmap-2024-11-20/src/pair.h:177:46: note: Function 'Pair_print_bedpe' argument 2 names different: declaration 'pairs_querydir' definition 'pairarray'.
gmap-2024-11-20/src/pair.c:3868:46: note: Function 'Pair_print_bedpe' argument 2 names different: declaration 'pairs_querydir' definition 'pairarray'.
gmap-2024-11-20/src/pair.c:7852:41: style:inconclusive: Function 'Pair_array_nmatches_posttrim' argument 1 names different: declaration 'pairs' definition 'pairarray'. [funcArgNamesDifferent]
gmap-2024-11-20/src/pair.h:291:41: note: Function 'Pair_array_nmatches_posttrim' argument 1 names different: declaration 'pairs' definition 'pairarray'.
gmap-2024-11-20/src/pair.c:7852:41: note: Function 'Pair_array_nmatches_posttrim' argument 1 names different: declaration 'pairs' definition 'pairarray'.
gmap-2024-11-20/src/pair.c:8427:17: style:inconclusive: Function 'Pair_fracidentity_bounded' argument 11 names different: declaration 'pairs' definition 'ptr'. [funcArgNamesDifferent]
gmap-2024-11-20/src/pair.h:320:17: note: Function 'Pair_fracidentity_bounded' argument 11 names different: declaration 'pairs' definition 'ptr'.
gmap-2024-11-20/src/pair.c:8427:17: note: Function 'Pair_fracidentity_bounded' argument 11 names different: declaration 'pairs' definition 'ptr'.
gmap-2024-11-20/src/pair.c:629:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:647:20: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:671:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:706:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:755:10: style: Parameter 'chrstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:757:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:784:13: style: Parameter 'chrstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:786:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:815:27: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:815:44: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:815:55: style: Parameter 'chrstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:913:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:1004:36: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:1666:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:1706:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:1739:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:1753:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:1954:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:1994:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:2179:33: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:2399:21: style: Variable 'old_token' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:2439:34: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:2923:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:3256:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:3752:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:3871:19: style: Variable 'ptr0' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:4445:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:4636:19: style: Variable 'ptr0' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:4636:26: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:4730:39: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:4742:47: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:4754:43: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:4773:51: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:4792:51: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:4812:59: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:4834:39: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:4857:47: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:5167:9: style: Variable 'token' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:5211:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:5504:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:6213:9: style: Variable 'cigar_token' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:6213:60: style: Variable 'first_token' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:7226:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:7270:39: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:7363:39: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:7512:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:8767:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:8795:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:8864:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:8938:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:9010:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:9071:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:9140:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:9210:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/pair.c:9455:46: style: Parameter 'pairarray' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:9473:44: style: Parameter 'pairarray' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:9492:55: style: Parameter 'pairarray' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pair.c:3808:14: warning: Uninitialized variable: querypos [uninitvar]
gmap-2024-11-20/src/pair.c:3798:27: note: Assuming condition is false
gmap-2024-11-20/src/pair.c:3808:14: note: Uninitialized variable: querypos
gmap-2024-11-20/src/pair.c:5084:22: error: Uninitialized variable: last_token [legacyUninitvar]
gmap-2024-11-20/src/pair.c:952:8: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:963:8: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:981:8: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:3901:20: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:5213:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:5506:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:6442:20: style: Variable 'cigar_tokens' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:9072:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:9141:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:9211:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:9565:18: style: Variable 'this' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:9638:16: style: Variable 'this' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pair.c:9925:9: style: Variable 'pairs' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-print-m8.c:285:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-print-m8.c:283:17: note: substring is assigned
gmap-2024-11-20/src/path-print-m8.c:285:17: note: substring is overwritten
gmap-2024-11-20/src/path-print-m8.c:294:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-print-m8.c:292:17: note: substring is assigned
gmap-2024-11-20/src/path-print-m8.c:294:17: note: substring is overwritten
gmap-2024-11-20/src/path-print-m8.c:304:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-print-m8.c:302:17: note: substring is assigned
gmap-2024-11-20/src/path-print-m8.c:304:17: note: substring is overwritten
gmap-2024-11-20/src/path-print-m8.c:312:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-print-m8.c:310:17: note: substring is assigned
gmap-2024-11-20/src/path-print-m8.c:312:17: note: substring is overwritten
gmap-2024-11-20/src/path-print-m8.c:285:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-print-m8.c:294:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-print-m8.c:304:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-print-m8.c:312:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-print-sam.c:314:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path-print-sam.c:515:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path-print-sam.c:2341:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path-print-alignment.c:752:21: style:inconclusive: Function 'Path_print_alignment' argument 4 names different: declaration 'shortread' definition 'queryseq'. [funcArgNamesDifferent]
gmap-2024-11-20/src/path-print-alignment.h:17:21: note: Function 'Path_print_alignment' argument 4 names different: declaration 'shortread' definition 'queryseq'.
gmap-2024-11-20/src/path-print-alignment.c:752:21: note: Function 'Path_print_alignment' argument 4 names different: declaration 'shortread' definition 'queryseq'.
gmap-2024-11-20/src/path-print-alignment.c:78:34: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path-print-alignment.c:95:42: style: Parameter 'nt' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path-print-alignment.c:172:26: style: Parameter 'genomic_diff' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path-trim.c:955:42: style: Redundant pointer operation on 'qend_nsegments' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-trim.c:955:61: style: Redundant pointer operation on 'qend_remainder' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-trim.c:1057:13: style: Variable 'nlow' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-trim.c:1075:15: style: Variable 'nlow' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-trim.c:1084:15: style: Variable 'nlow' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path.c:591:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path.c:601:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path.c:618:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path.c:649:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path.c:453:3: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
gmap-2024-11-20/src/path.c:1302:57: style: Redundant pointer operation on 'new_pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path.c:1437:57: style: Redundant pointer operation on 'B_pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path.c:2696:22: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path.c:2716:25: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path.c:871:56: style:inconclusive: Function 'Path_fill_main_univdiagonal' argument 2 names different: declaration 'cumsum' definition 'indices'. [funcArgNamesDifferent]
gmap-2024-11-20/src/path.h:359:56: note: Function 'Path_fill_main_univdiagonal' argument 2 names different: declaration 'cumsum' definition 'indices'.
gmap-2024-11-20/src/path.c:871:56: note: Function 'Path_fill_main_univdiagonal' argument 2 names different: declaration 'cumsum' definition 'indices'.
gmap-2024-11-20/src/path.c:1273:30: style: Parameter 'old' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path.c:1273:48: style: Parameter 'end_old' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path.c:1275:34: style: Parameter 'end_new' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path.c:1279:16: style: Variable 'new_start' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/path.c:1415:21: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path.c:1415:37: style: Parameter 'end_A' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path.c:1417:21: style: Parameter 'B' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path.c:1417:37: style: Parameter 'end_B' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/path.c:1421:16: style: Variable 'out_start' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/path.c:1230:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path.c:1839:13: style: Unused variable: q [unusedVariable]
gmap-2024-11-20/src/path.c:1951:13: style: Unused variable: q [unusedVariable]
gmap-2024-11-20/src/path.c:2105:13: style: Unused variable: q [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:2040:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pathpair-eval.c:1400:25: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:1400:43: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:1469:25: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:1469:43: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:1614:55: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:1630:53: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:1709:56: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:1725:54: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair-eval.c:160:8: style: Unused variable: overlappingp_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:160:24: style: Unused variable: overlappingp_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:161:8: style: Unused variable: insertlength_knownp_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:161:31: style: Unused variable: insertlength_knownp_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:162:5: style: Unused variable: outerlength_knownp_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:162:27: style: Unused variable: outerlength_knownp_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:382:7: style: Unused variable: chop_qstart_5 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:382:22: style: Unused variable: chop_qend_5 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:382:35: style: Unused variable: chop_qstart_3 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:382:50: style: Unused variable: chop_qend_3 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:383:7: style: Unused variable: chopped_nmatches_a [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:383:27: style: Unused variable: chopped_nmatches_b [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:396:8: style: Unused variable: overlappingp_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:396:24: style: Unused variable: overlappingp_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:397:8: style: Unused variable: insertlength_knownp_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:397:31: style: Unused variable: insertlength_knownp_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:398:5: style: Unused variable: outerlength_knownp_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:398:27: style: Unused variable: outerlength_knownp_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:816:7: style: Unused variable: chop_qstart_5 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:816:22: style: Unused variable: chop_qend_5 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:816:35: style: Unused variable: chop_qstart_3 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:816:50: style: Unused variable: chop_qend_3 [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:817:7: style: Unused variable: chopped_nmatches_a [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:817:27: style: Unused variable: chopped_nmatches_b [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:820:7: style: Unused variable: coverage_a [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:820:19: style: Unused variable: coverage_b [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:822:12: style: Unused variable: insertlength_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:822:28: style: Unused variable: insertlength_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:823:12: style: Unused variable: outerlength_x [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:823:27: style: Unused variable: outerlength_y [unusedVariable]
gmap-2024-11-20/src/pathpair-eval.c:1863:18: style: Variable 'junction_prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pathpair-eval.c:1864:18: style: Variable 'junction_prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pathpair-eval.c:1889:18: style: Variable 'junction_prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pathpair-eval.c:1890:18: style: Variable 'junction_prob' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pathpair-eval.c:2186:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pathpair.c:3154:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pathpair.c:3414:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/path-solve.c:2593:11: style: Condition '1||newpaths==NULL' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/path-solve.c:2987:11: style: Condition '1||newpaths==NULL' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/path-solve.c:3909:9: style: Condition '0&&nmismatches>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-solve.c:2040:13: style: Variable 'qend1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-solve.c:2000:13: note: qend1 is assigned
gmap-2024-11-20/src/path-solve.c:2040:13: note: qend1 is overwritten
gmap-2024-11-20/src/path-solve.c:2039:15: style: Variable 'qstart1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-solve.c:2001:15: note: qstart1 is assigned
gmap-2024-11-20/src/path-solve.c:2039:15: note: qstart1 is overwritten
gmap-2024-11-20/src/path-solve.c:2044:15: style: Variable 'qstart2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-solve.c:2003:15: note: qstart2 is assigned
gmap-2024-11-20/src/path-solve.c:2044:15: note: qstart2 is overwritten
gmap-2024-11-20/src/path-solve.c:2045:13: style: Variable 'qend2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/path-solve.c:2004:13: note: qend2 is assigned
gmap-2024-11-20/src/path-solve.c:2045:13: note: qend2 is overwritten
gmap-2024-11-20/src/path-solve.c:4049:10: style: Variable 'auxinfo->qstart' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2024-11-20/src/path-solve.c:4037:10: note: qstart is assigned 'auxinfo->qstart' here.
gmap-2024-11-20/src/path-solve.c:4049:10: note: Variable 'auxinfo->qstart' is assigned an expression that holds the same value.
gmap-2024-11-20/src/path-solve.c:2322:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:2778:25: style: Redundant pointer operation on 'qstart_paths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:3185:23: style: Redundant pointer operation on 'qend_paths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:3685:52: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:3715:56: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:4053:29: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:4055:8: style: Redundant pointer operation on 'unextended_sense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:4055:35: style: Redundant pointer operation on 'unextended_antisense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:4056:8: style: Redundant pointer operation on 'complete_sense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:4056:33: style: Redundant pointer operation on 'complete_antisense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:4223:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:5044:22: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:5852:22: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:6221:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-solve.c:3290:19: style:inconclusive: Function 'Path_solve_from_diagonals' argument 6 names different: declaration 'middle_diagonal_univdiagonal' definition 'middle_univdiagonal'. [funcArgNamesDifferent]
gmap-2024-11-20/src/path-solve.h:62:19: note: Function 'Path_solve_from_diagonals' argument 6 names different: declaration 'middle_diagonal_univdiagonal' definition 'middle_univdiagonal'.
gmap-2024-11-20/src/path-solve.c:3290:19: note: Function 'Path_solve_from_diagonals' argument 6 names different: declaration 'middle_diagonal_univdiagonal' definition 'middle_univdiagonal'.
gmap-2024-11-20/src/path-solve.c:4291:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/path-solve.c:5072:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/path-solve.c:1203:37: style: Unused variable: nmismatches_indel [unusedVariable]
gmap-2024-11-20/src/path-solve.c:1204:43: style: Unused variable: ref_nmismatches_indel [unusedVariable]
gmap-2024-11-20/src/path-solve.c:2121:12: style: Variable 'ninserts2' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-solve.c:2465:22: style: Variable 'qstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-solve.c:2859:20: style: Variable 'qend' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-solve.c:3315:10: style: Unused variable: repaired_paths [unusedVariable]
gmap-2024-11-20/src/path-solve.c:3889:23: style: Variable 'perfect_ends_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-solve.c:5873:37: style: Unused variable: nmismatches_indel [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5874:43: style: Unused variable: ref_nmismatches_indel [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5876:10: style: Unused variable: donor_prob [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5876:22: style: Unused variable: acceptor_prob [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5878:7: style: Unused variable: type [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5879:7: style: Unused variable: trimpos5 [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5879:17: style: Unused variable: trimpos3 [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5879:27: style: Unused variable: supporti [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5879:37: style: Unused variable: supportj [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5880:7: style: Unused variable: splice_qpos [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5881:47: style: Unused variable: univdiagonal_k [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5883:12: style: Unused variable: splice_distance [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5885:7: style: Unused variable: ignore [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5890:14: style: Unused variable: splice_junction [unusedVariable]
gmap-2024-11-20/src/path-solve.c:5890:31: style: Unused variable: indel_junction [unusedVariable]
gmap-2024-11-20/src/pathstore.c:111:32: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathstore.c:420:32: style: Redundant pointer operation on 'new' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathstore.c:568:41: style: Parameter 'univdiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pathpair.c:563:84: style: Condition '(offset=((*cutpointH)-queryendH)-(segmentL_high-queryendL))<0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/pathpair.c:603:82: style: Condition '(offset=((*cutpointH)-queryendH)-(segmentL_high-queryendL))<0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/pathpair.c:666:89: style: Condition '(offset=((segmentH_low-querystartH)-((*cutpointL)-querystartL)))<0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/pathpair.c:714:87: style: Condition '(offset=((segmentH_low-querystartH)-((*cutpointL)-querystartL)))<0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/pathpair.c:980:19: style: Condition 'junctionH!=NULL' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/pathpair.c:1097:19: style: Condition 'junctionL!=NULL' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/pathpair.c:3282:7: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/pathpair.c:3287:9: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/pathpair.c:3282:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/pathpair.c:129:25: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:976:26: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1069:24: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1093:26: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1163:24: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1290:23: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1348:25: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1486:21: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1491:21: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1563:21: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:1629:21: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/pathpair.c:490:25: style: Parameter 'queryseq1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pathpair.c:491:11: style: Parameter 'queryseq2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/pathpair.c:781:36: style: Unused variable: junction [unusedVariable]
gmap-2024-11-20/src/pathpair.c:3310:7: style: Variable 'npaths_primary' is not assigned a value. [unassignedVariable]
gmap-2024-11-20/src/pbinom.c:720:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:739:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:824:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:899:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1004:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1041:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1064:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1164:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1317:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1392:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1421:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1478:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1642:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/pbinom.c:1412:12: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
gmap-2024-11-20/src/pbinom.c:141:7: style: struct member 'cheb_series_struct::order_sp' is never used. [unusedStructMember]
gmap-2024-11-20/src/pbinom.c:176:20: style: struct member 'Anonymous0::n' is never used. [unusedStructMember]
gmap-2024-11-20/src/pbinom.c:176:38: style: struct member 'Anonymous0::i' is never used. [unusedStructMember]
gmap-2024-11-20/src/pbinom.c:154:12: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pbinom.c:159:7: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/pbinom.c:166:7: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/printbuffer.c:446:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/printbuffer.c:323:17: style: Redundant pointer operation on 'output_list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/repair.c:449:22: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/repair.c:48:10: style:inconclusive: Function 'Repair_new' argument 2 names different: declaration 'trstart_overhang' definition 'tstart_overhang'. [funcArgNamesDifferent]
gmap-2024-11-20/src/repair.h:44:10: note: Function 'Repair_new' argument 2 names different: declaration 'trstart_overhang' definition 'tstart_overhang'.
gmap-2024-11-20/src/repair.c:48:10: note: Function 'Repair_new' argument 2 names different: declaration 'trstart_overhang' definition 'tstart_overhang'.
gmap-2024-11-20/src/repair.c:48:36: style:inconclusive: Function 'Repair_new' argument 3 names different: declaration 'trstart_splice_distance' definition 'tstart_splice_distance'. [funcArgNamesDifferent]
gmap-2024-11-20/src/repair.h:44:37: note: Function 'Repair_new' argument 3 names different: declaration 'trstart_splice_distance' definition 'tstart_splice_distance'.
gmap-2024-11-20/src/repair.c:48:36: note: Function 'Repair_new' argument 3 names different: declaration 'trstart_splice_distance' definition 'tstart_splice_distance'.
gmap-2024-11-20/src/repetitive.c:908:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/resulthr.c:72:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/resulthr.c:101:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/resulthr.c:239:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/saca-k.c:455:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/saca-k.c:154:33: style: Condition 'SA[h]==EMPTY' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/saca-k.c:154:23: note: Assuming that condition 'SA[h]>=0' is not redundant
gmap-2024-11-20/src/saca-k.c:154:33: note: Condition 'SA[h]==EMPTY' is always false
gmap-2024-11-20/src/saca-k.c:200:16: style: Condition 'j!=EMPTY' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/saca-k.c:200:9: note: Assuming that condition 'j<0' is not redundant
gmap-2024-11-20/src/saca-k.c:200:16: note: Condition 'j!=EMPTY' is always true
gmap-2024-11-20/src/saca-k.c:229:33: style: Condition 'SA[h]==EMPTY' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/saca-k.c:229:23: note: Assuming that condition 'SA[h]>=0' is not redundant
gmap-2024-11-20/src/saca-k.c:229:33: note: Condition 'SA[h]==EMPTY' is always false
gmap-2024-11-20/src/saca-k.c:274:18: style: Condition 'j!=EMPTY' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/saca-k.c:274:11: note: Assuming that condition 'j<0' is not redundant
gmap-2024-11-20/src/saca-k.c:274:18: note: Condition 'j!=EMPTY' is always true
gmap-2024-11-20/src/saca-k.c:341:16: style: Condition 'j!=EMPTY' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/saca-k.c:341:9: note: Assuming that condition 'j<0' is not redundant
gmap-2024-11-20/src/saca-k.c:341:16: note: Condition 'j!=EMPTY' is always true
gmap-2024-11-20/src/saca-k.c:65:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bkt [nullPointerOutOfMemory]
gmap-2024-11-20/src/saca-k.c:460:31: note: Assuming allocation function fails
gmap-2024-11-20/src/saca-k.c:460:9: note: Assignment 'bkt=(unsigned int*)malloc(sizeof(int)*K)', assigned value is 0
gmap-2024-11-20/src/saca-k.c:462:23: note: Calling function 'induceSAl0', 3rd argument 'bkt' value is 0
gmap-2024-11-20/src/saca-k.c:65:3: note: Null pointer dereference
gmap-2024-11-20/src/saca-k.c:24:32: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/saca-k.c:120:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/saca-k.c:133:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/saca-k.c:208:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/saca-k.c:282:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/samheader.c:99:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/samheader.c:289:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/samheader.c:310:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/samheader.c:257:3: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/samheader.c:259:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/samheader.c:257:3: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/samheader.c:82:11: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/samheader.c:84:9: style: Variable 'write_mode' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/samheader.c:85:20: style: Variable 'suffix' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sarray-write.c:97:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sarray-write.c:648:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sarray-write.c:743:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sarray-write.c:1028:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sarray-write.c:1252:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sarray-write.c:2437:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sarray-write.c:2637:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sarray-write.c:2799:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sedgesort.c:177:73: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2024-11-20/src/sedgesort.c:238:62: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2024-11-20/src/sedgesort.c:300:63: style: Parameter 'array1' can be declared as const array [constParameter]
gmap-2024-11-20/src/sedgesort.c:300:86: style: Parameter 'array2' can be declared as const array [constParameter]
gmap-2024-11-20/src/segmentpos.c:163:30: style: Parameter 'indices' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/segmentpos.c:164:33: style: Parameter 'align_strain' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/segmentpos.c:197:9: style: Parameter 'align_strain' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:707:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:706:15: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:706:15: note: Assignment 'fp=fopen(indexcompfile,"w")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:707:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:708:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:706:15: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:706:15: note: Assignment 'fp=fopen(indexcompfile,"w")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:708:12: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:744:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:741:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:741:13: note: Assignment 'fp=fopen(sasampleqfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:744:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:745:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:741:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:741:13: note: Assignment 'fp=fopen(sasampleqfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:745:10: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:785:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:785:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:786:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:786:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:787:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:787:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:788:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:788:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:789:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:789:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:792:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:792:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:794:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:784:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:794:10: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:808:3: warning: If resource allocation fails, then there is a possible null pointer dereference: sa_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:802:16: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:802:16: note: Assignment 'sa_fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:808:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:809:3: warning: If resource allocation fails, then there is a possible null pointer dereference: samples_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:803:21: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:803:21: note: Assignment 'samples_fp=fopen(sasamplesfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:809:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:815:5: warning: If resource allocation fails, then there is a possible null pointer dereference: sa_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:802:16: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:802:16: note: Assignment 'sa_fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:815:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:828:5: warning: If resource allocation fails, then there is a possible null pointer dereference: sa_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:802:16: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:802:16: note: Assignment 'sa_fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:828:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:846:14: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:845:17: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:845:17: note: Assignment 'fp=fopen(csaptrfiles[chari],"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:846:14: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:848:14: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:847:17: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:847:17: note: Assignment 'fp=fopen(csacompfiles[chari],"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:848:14: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1022:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1018:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1018:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1022:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1033:5: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1018:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1018:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1033:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1037:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1018:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1018:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1037:10: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1045:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1042:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1042:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1045:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1051:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1042:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1042:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1051:10: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1064:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1059:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1059:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1064:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1077:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1060:20: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1060:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1077:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1080:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1059:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1059:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1080:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1111:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1102:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1102:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1111:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1112:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1103:20: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1103:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1112:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1246:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1242:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1242:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1246:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1257:5: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1242:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1242:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1257:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1261:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1242:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1242:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1261:10: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1269:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1266:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1266:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1269:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1273:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1266:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1266:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1273:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1275:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1266:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1266:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1275:10: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1288:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1283:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1283:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1288:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1301:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1284:20: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1284:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"wb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1301:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1304:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1283:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1283:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1304:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1335:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1326:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1326:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1335:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:1336:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:1327:20: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:1327:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:1336:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:2318:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:2317:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:2317:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:2318:3: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:2321:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/sarray-write.c:2317:13: note: Assuming allocation function fails
gmap-2024-11-20/src/sarray-write.c:2317:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2024-11-20/src/sarray-write.c:2321:5: note: Null pointer dereference
gmap-2024-11-20/src/sarray-write.c:3021:12: style: Variable 'plcpcomp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/sarray-write.c:3020:12: note: plcpcomp is assigned
gmap-2024-11-20/src/sarray-write.c:3021:12: note: plcpcomp is overwritten
gmap-2024-11-20/src/sarray-write.c:3084:9: style: Variable 'lcp_i' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/sarray-write.c:3034:9: note: lcp_i is assigned
gmap-2024-11-20/src/sarray-write.c:3084:9: note: lcp_i is overwritten
gmap-2024-11-20/src/sarray-write.c:83:27: style: Parameter 'sarrayfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:88:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sarray-write.c:265:74: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:266:54: style: Parameter 'SA' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:724:66: style: Parameter 'sasampleqfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:724:87: style: Parameter 'sasamplesfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:724:108: style: Parameter 'saindex0file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:726:21: style: Variable 'SA_inv' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sarray-write.c:999:44: style: Parameter 'rankfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:999:60: style: Parameter 'permuted_sarray_file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:1002:10: style: Variable 'SA' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sarray-write.c:1007:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sarray-write.c:1221:12: style: Parameter 'rankfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:1221:28: style: Parameter 'permuted_sarray_file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:1226:10: style: Variable 'SA' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sarray-write.c:1231:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sarray-write.c:2297:51: style: Parameter 'sarrayfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sarray-write.c:2999:10: style: Variable 'SA' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/semaphore.c:23:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IPC_CREAT [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/semaphore.c:41:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/semaphore.c:57:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SETVAL [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/semaphore.c:83:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEM_UNDO [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/semaphore.c:96:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEM_UNDO [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/semaphore.c:84:3: warning: Return value of function semop() is not used. [ignoredReturnValue]
gmap-2024-11-20/src/semaphore.c:97:3: warning: Return value of function semop() is not used. [ignoredReturnValue]
gmap-2024-11-20/src/semaphore.c:15:49: style:inconclusive: Function 'Semaphore_create' argument 3 names different: declaration 'vals' definition 'values'. [funcArgNamesDifferent]
gmap-2024-11-20/src/semaphore.h:21:49: note: Function 'Semaphore_create' argument 3 names different: declaration 'vals' definition 'values'.
gmap-2024-11-20/src/semaphore.c:15:49: note: Function 'Semaphore_create' argument 3 names different: declaration 'vals' definition 'values'.
gmap-2024-11-20/src/semaphore.c:18:9: style: union member 'semun::val' is never used. [unusedStructMember]
gmap-2024-11-20/src/semaphore.c:19:22: style: union member 'semun::buf' is never used. [unusedStructMember]
gmap-2024-11-20/src/semaphore.c:52:22: style: union member 'semun::buf' is never used. [unusedStructMember]
gmap-2024-11-20/src/semaphore.c:53:13: style: union member 'semun::array' is never used. [unusedStructMember]
gmap-2024-11-20/src/semaphore.c:81:14: style: Variable 'op.sem_num' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/semaphore.c:82:13: style: Variable 'op.sem_op' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/semaphore.c:83:14: style: Variable 'op.sem_flg' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/semaphore.c:94:14: style: Variable 'op.sem_num' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/semaphore.c:95:13: style: Variable 'op.sem_op' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/semaphore.c:96:14: style: Variable 'op.sem_flg' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/sequence.c:544:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sequence.c:814:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sequence.c:916:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sequence.c:1412:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sequence.c:1580:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sequence.c:1705:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sequence.c:1927:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:274:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:402:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:700:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:993:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:1137:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:2682:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:3483:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:3838:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:4521:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:4542:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:4559:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:4575:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:4587:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:5244:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/shortread.c:5290:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/sequence.c:642:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/sequence.c:650:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/sequence.c:718:7: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/sequence.c:721:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/sequence.c:852:2: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/sequence.c:866:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/sequence.c:869:4: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/sequence.c:876:18: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/sequence.c:950:2: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/sequence.c:963:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/sequence.c:966:4: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/sequence.c:973:18: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/sequence.c:2157:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/sequence.c:1732:24: style: Expression is always true because 'else if' condition is opposite to previous condition at line 1721. [multiCondition]
gmap-2024-11-20/src/sequence.c:1721:24: note: first condition
gmap-2024-11-20/src/sequence.c:1732:24: note: else if condition is opposite to first condition
gmap-2024-11-20/src/sequence.c:1041:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1047:36: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1047:49: style: Redundant pointer operation on 'pointer2a' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1047:63: style: Redundant pointer operation on 'length2a' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1048:8: style: Redundant pointer operation on 'pointer2b' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1048:22: style: Redundant pointer operation on 'length2b' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1466:36: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1538:37: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:1608:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/sequence.c:166:18: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sequence.c:180:18: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sequence.c:680:9: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/sequence.c:1109:24: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sequence.c:1122:21: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sequence.c:1300:23: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/sequence.c:1305:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2024-11-20/src/sequence.c:1870:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2024-11-20/src/sequence.c:1909:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2024-11-20/src/sequence.c:1965:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2024-11-20/src/sequence.c:2011:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2024-11-20/src/path-print-sam.c:773:17: style: Redundant pointer operation on 'hardclip_low' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:773:34: style: Redundant pointer operation on 'hardclip_high' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2045:20: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2056:20: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2181:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2192:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2299:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2310:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2353:25: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2364:25: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2414:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2425:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2460:25: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2475:25: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2549:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2561:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2585:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2621:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2661:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2689:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2729:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2757:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2866:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2881:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2924:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2935:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:2999:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:3010:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:3053:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:3064:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:1866:37: style:inconclusive: Function 'Path_print_sam' argument 16 names different: declaration 'queryseq_mate' definition 'mate_queryseq'. [funcArgNamesDifferent]
gmap-2024-11-20/src/path-print-sam.h:32:37: note: Function 'Path_print_sam' argument 16 names different: declaration 'queryseq_mate' definition 'mate_queryseq'.
gmap-2024-11-20/src/path-print-sam.c:1866:37: note: Function 'Path_print_sam' argument 16 names different: declaration 'queryseq_mate' definition 'mate_queryseq'.
gmap-2024-11-20/src/path-print-sam.c:759:16: style: Variable 'alts_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:413:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/shortread.c:421:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/shortread.c:711:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/shortread.c:719:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/shortread.c:1002:7: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/shortread.c:1005:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/shortread.c:1106:8: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/shortread.c:1158:4: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/shortread.c:1169:23: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/shortread.c:5254:17: style: Condition 'shift==0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/shortread.c:5300:17: style: Condition 'shift==0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/path-print-sam.c:2179:41: error: Uninitialized variable: clipdir [legacyUninitvar]
gmap-2024-11-20/src/shortread.c:2738:45: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2744:29: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2756:45: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2756:58: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2766:40: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2766:53: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2771:16: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2774:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2774:48: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2785:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2785:48: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2813:42: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2825:29: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2839:55: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2850:20: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2853:39: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2853:52: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2874:20: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2877:50: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2910:18: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2913:37: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:2913:50: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3893:42: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3901:45: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3907:35: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3914:39: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3914:52: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3929:14: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3932:33: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3932:46: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3952:37: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3975:45: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3990:16: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:3993:46: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4431:44: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4431:57: style: Redundant pointer operation on 'queryseq2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4431:71: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4432:28: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4432:38: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4457:38: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4457:51: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4457:63: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4457:75: style: Redundant pointer operation on 'queryseq2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4458:10: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4458:21: style: Redundant pointer operation on 'input2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4458:51: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4458:61: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4487:38: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4487:51: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4487:63: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4487:75: style: Redundant pointer operation on 'queryseq2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4488:10: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4488:21: style: Redundant pointer operation on 'input2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4488:51: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/shortread.c:4488:61: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/path-print-sam.c:217:14: style: Variable 'ninserts' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/shortread.c:369:9: style:inconclusive: Function 'Shortread_setup' argument 3 names different: declaration 'force_singled_end_p_in' definition 'force_single_end_p_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/shortread.h:26:9: note: Function 'Shortread_setup' argument 3 names different: declaration 'force_singled_end_p_in' definition 'force_single_end_p_in'.
gmap-2024-11-20/src/shortread.c:369:9: note: Function 'Shortread_setup' argument 3 names different: declaration 'force_singled_end_p_in' definition 'force_single_end_p_in'.
gmap-2024-11-20/src/path-print-sam.c:422:12: style: Variable 'ninserts' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/path-print-sam.c:759:36: style: Unused variable: medial_univdiagonal [unusedVariable]
gmap-2024-11-20/src/path-print-sam.c:761:15: style: Unused variable: chroffset [unusedVariable]
gmap-2024-11-20/src/path-print-sam.c:1125:15: style: Unused variable: chroffset [unusedVariable]
gmap-2024-11-20/src/path-print-sam.c:1364:15: style: Unused variable: chroffset [unusedVariable]
gmap-2024-11-20/src/shortread.c:397:26: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:694:23: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:991:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:1103:34: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/shortread.c:1407:24: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/shortread.c:1438:21: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/shortread.c:1455:23: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/shortread.c:1460:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2024-11-20/src/shortread.c:2085:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:2183:9: style: Variable 'contents1' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:2184:9: style: Variable 'contents2' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:2279:9: style: Variable 'contents1' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:2280:9: style: Variable 'contents2' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:2345:9: style: Variable 'contents1' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:2346:9: style: Variable 'contents2' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/shortread.c:3470:70: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/single-cell.c:65:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/single-cell.c:161:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/single-cell.c:351:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/single-cell.c:711:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:69:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:74:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:170:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:722:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:1014:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:1200:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:1490:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:1513:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:1547:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:1764:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/single-cell.c:74:7: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/single-cell.c:77:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2024-11-20/src/single-cell.c:135:8: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/single-cell.c:179:2: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/single-cell.c:187:23: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2024-11-20/src/single-cell.c:682:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/single-cell.c:674:13: note: Assuming allocation function fails
gmap-2024-11-20/src/single-cell.c:674:13: note: Assignment 'fp=fopen(whitelist_file,"r")', assigned value is 0
gmap-2024-11-20/src/single-cell.c:682:10: note: Null pointer dereference
gmap-2024-11-20/src/single-cell.c:392:45: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:398:21: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:404:39: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:404:52: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:409:16: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:412:18: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:412:31: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:625:39: style: Redundant pointer operation on 'whitelist_total' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:626:11: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:626:24: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:626:36: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:627:30: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:627:40: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/single-cell.c:63:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/single-cell.c:132:34: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/single-cell.c:634:9: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/single-cell.c:635:9: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/single-cell.c:657:35: style: Parameter 'whitelist_file' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/single-cell.c:776:50: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/single-cell.c:776:66: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/single-cell.c:857:16: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/single-cell.c:404:23: style: Variable 'fulllength' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/smooth.c:129:34: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:130:35: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:131:36: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:194:35: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:300:36: style: Redundant pointer operation on 'nintrons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:333:38: style: Redundant pointer operation on 'nintrons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:334:41: style: Redundant pointer operation on 'nintrons' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:960:36: style: Redundant pointer operation on 'deletep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:1046:34: style: Redundant pointer operation on 'shortp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:1200:34: style: Redundant pointer operation on 'badp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/smooth.c:392:60: style: Parameter 'intronlengths' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:428:70: style: Parameter 'exonmatches' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:476:15: style: Parameter 'exonmatches' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:476:33: style: Parameter 'exonprotects' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:477:15: style: Parameter 'intronlengths' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:590:66: style: Parameter 'exonmatches' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:591:16: style: Parameter 'donor_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:591:37: style: Parameter 'acceptor_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:592:13: style: Parameter 'intron_matches_left' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:592:39: style: Parameter 'intron_denominator_left' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:593:13: style: Parameter 'intron_matches_right' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:593:40: style: Parameter 'intron_denominator_right' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/smooth.c:747:15: style: Parameter 'exonstatus' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:158:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:221:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:241:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:381:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:731:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:942:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:1173:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:1293:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:1384:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/snpindex.c:1920:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/simplepair.c:1357:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2024-11-20/src/simplepair.c:1828:14: style: Condition 'chrnum!=0' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/simplepair.c:139:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/simplepair.c:686:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/simplepair.c:970:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2024-11-20/src/simplepair.c:395:17: style: Redundant pointer operation on 'tokens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/simplepair.c:1129:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/simplepair.c:1129:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/simplepair.c:1129:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/simplepair.c:1132:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/simplepair.c:1132:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/simplepair.c:1132:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/simplepair.c:1749:16: style: Local variable 'flag' shadows outer argument [shadowArgument]
gmap-2024-11-20/src/simplepair.c:1739:45: note: Shadowed declaration
gmap-2024-11-20/src/simplepair.c:1749:16: note: Shadow variable
gmap-2024-11-20/src/simplepair.c:378:34: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:418:9: style: Variable 'token' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/simplepair.c:530:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/simplepair.c:811:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/simplepair.c:1146:9: style: Variable 'cigar_token' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/simplepair.c:1146:60: style: Variable 'first_token' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/simplepair.c:1376:39: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:1388:47: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:1400:43: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:1419:51: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:1438:51: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:1458:59: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:1480:39: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:1503:47: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/simplepair.c:447:22: error: Uninitialized variable: last_token [legacyUninitvar]
gmap-2024-11-20/src/simplepair.c:348:14: style: Variable 'highpair' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/simplepair.c:363:14: style: Variable 'highpair' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/simplepair.c:532:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/simplepair.c:813:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/simplepair.c:1357:18: style: Variable 'cigar_tokens' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/snpindex.c:1496:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2024-11-20/src/snpindex.c:1831:23: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2024-11-20/src/snpindex.c:1827:23: note: First condition
gmap-2024-11-20/src/snpindex.c:1831:23: note: Second condition
gmap-2024-11-20/src/snpindex.c:212:44: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:322:9: style: Variable 'snptype' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:677:45: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:690:22: style: Parameter 'output_offsetsmetafile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:690:52: style: Parameter 'output_offsetsstrmfile' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:1085:86: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:1088:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:1120:27: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:1120:55: style: Parameter 'end2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:1124:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:1124:26: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:1230:61: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:1231:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:1253:61: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:1254:27: style: Parameter 'end2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/snpindex.c:1255:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:1255:26: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:1337:28: style: Variable 'destdir' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/snpindex.c:313:15: style: Unused variable: centerp [unusedVariable]
gmap-2024-11-20/src/snpindex.c:894:16: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/snpindex.c:1368:7: style: Unused variable: ref_offsetsmeta_fd [unusedVariable]
gmap-2024-11-20/src/snpindex.c:1368:27: style: Unused variable: ref_offsetsstrm_fd [unusedVariable]
gmap-2024-11-20/src/snpindex.c:1368:47: style: Unused variable: ref_positions_high_fd [unusedVariable]
gmap-2024-11-20/src/snpindex.c:1368:70: style: Unused variable: ref_positions_fd [unusedVariable]
gmap-2024-11-20/src/snpindex.c:1369:5: style: Unused variable: snponly_offsetsmeta_fd [unusedVariable]
gmap-2024-11-20/src/snpindex.c:1369:29: style: Unused variable: snponly_offsetsstrm_fd [unusedVariable]
gmap-2024-11-20/src/spliceendsgen.c:114:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/spliceendsgen.c:148:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/spliceends.c:792:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable univdiagonal [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/spliceends.c:3138:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/spliceends.c:3378:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable univdiagonal [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/spliceends.c:5495:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie.c:207:48: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:305:43: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:392:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:394:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:394:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:394:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:395:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:395:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:395:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:395:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:396:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:399:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:405:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:407:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:407:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:407:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:408:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:408:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:408:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:408:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:409:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:412:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:418:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:420:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:420:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:420:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:421:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:421:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:421:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:421:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:422:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:425:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:431:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:433:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:433:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:433:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:434:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:434:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:434:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:434:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:435:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:438:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:494:48: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:589:43: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:673:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:675:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:675:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:675:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:676:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:676:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:676:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:676:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:677:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:680:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:686:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:688:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:688:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:688:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:689:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:689:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:689:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:689:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:690:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:693:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:699:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:701:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:701:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:701:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:702:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:702:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:702:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:702:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:703:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:706:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:712:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:714:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:714:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:714:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:715:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:715:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:715:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:715:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:716:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:719:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:766:5: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:766:20: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:766:33: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:767:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:767:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:767:28: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:767:45: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:768:5: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:771:23: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:833:5: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:833:20: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:833:33: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:834:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:834:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:834:28: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:834:45: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:835:5: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:838:23: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie.c:239:27: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splicetrie.c:276:31: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splicetrie.c:524:27: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splicetrie.c:560:31: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splicetrie_build.c:425:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:853:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:1396:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:1557:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:2043:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:2384:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:2805:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:3112:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:3383:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splicetrie_build.c:771:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/splicetrie_build.c:1586:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie_build.c:1589:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie_build.c:1592:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie_build.c:1595:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splicetrie_build.c:190:34: style: Parameter 'buffer' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:238:35: style: Parameter 'buffer' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:384:54: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:805:50: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:1859:22: style: Parameter 'splicesites' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:1859:49: style: Parameter 'splicetypes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:1860:19: style: Parameter 'splicedists' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:2062:13: style: Parameter 'nsplicepartners_skip' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:2062:40: style: Parameter 'nsplicepartners_obs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:2062:66: style: Parameter 'nsplicepartners_max' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:2063:22: style: Parameter 'splicetypes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:2864:58: style: Parameter 'splicesites' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:2864:85: style: Parameter 'splicetypes' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:2866:56: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splicetrie_build.c:1282:18: style: struct member 'Trie_T::leaf' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1284:7: style: struct member 'Trie_T::nsites' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1285:7: style: struct member 'Trie_T::na' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1286:7: style: struct member 'Trie_T::nc' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1287:7: style: struct member 'Trie_T::ng' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1288:7: style: struct member 'Trie_T::nt' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1290:10: style: struct member 'Trie_T::triea' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1291:10: style: struct member 'Trie_T::triec' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1292:10: style: struct member 'Trie_T::trieg' is never used. [unusedStructMember]
gmap-2024-11-20/src/splicetrie_build.c:1293:10: style: struct member 'Trie_T::triet' is never used. [unusedStructMember]
gmap-2024-11-20/src/spliceends.c:2906:16: style: The comparison 'donep == 0' is always true. [knownConditionTrueFalse]
gmap-2024-11-20/src/spliceends.c:2874:16: note: 'donep' is assigned value '0' here.
gmap-2024-11-20/src/spliceends.c:2906:16: note: The comparison 'donep == 0' is always true.
gmap-2024-11-20/src/spliceends.c:5257:16: style: The comparison 'donep == 0' is always true. [knownConditionTrueFalse]
gmap-2024-11-20/src/spliceends.c:5224:16: note: 'donep' is assigned value '0' here.
gmap-2024-11-20/src/spliceends.c:5257:16: note: The comparison 'donep == 0' is always true.
gmap-2024-11-20/src/spliceends.c:5592:16: style: The comparison 'donep == 0' is always true. [knownConditionTrueFalse]
gmap-2024-11-20/src/spliceends.c:5559:16: note: 'donep' is assigned value '0' here.
gmap-2024-11-20/src/spliceends.c:5592:16: note: The comparison 'donep == 0' is always true.
gmap-2024-11-20/src/spliceends.c:6045:16: style: The comparison 'donep == 0' is always true. [knownConditionTrueFalse]
gmap-2024-11-20/src/spliceends.c:6011:16: note: 'donep' is assigned value '0' here.
gmap-2024-11-20/src/spliceends.c:6045:16: note: The comparison 'donep == 0' is always true.
gmap-2024-11-20/src/spliceends.c:2898:11: style: Redundant initialization for 'trimpos'. The initialized value is overwritten before it is read. [redundantInitialization]
gmap-2024-11-20/src/spliceends.c:2873:15: note: trimpos is initialized
gmap-2024-11-20/src/spliceends.c:2898:11: note: trimpos is overwritten
gmap-2024-11-20/src/spliceends.c:5249:11: style: Redundant initialization for 'trimpos'. The initialized value is overwritten before it is read. [redundantInitialization]
gmap-2024-11-20/src/spliceends.c:5223:15: note: trimpos is initialized
gmap-2024-11-20/src/spliceends.c:5249:11: note: trimpos is overwritten
gmap-2024-11-20/src/spliceends.c:5584:11: style: Redundant initialization for 'trimpos'. The initialized value is overwritten before it is read. [redundantInitialization]
gmap-2024-11-20/src/spliceends.c:5558:15: note: trimpos is initialized
gmap-2024-11-20/src/spliceends.c:5584:11: note: trimpos is overwritten
gmap-2024-11-20/src/spliceends.c:6037:11: style: Redundant initialization for 'trimpos'. The initialized value is overwritten before it is read. [redundantInitialization]
gmap-2024-11-20/src/spliceends.c:6010:15: note: trimpos is initialized
gmap-2024-11-20/src/spliceends.c:6037:11: note: trimpos is overwritten
gmap-2024-11-20/src/spliceends.c:1776:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1777:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1830:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1831:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1869:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1870:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1886:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1887:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:1999:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2000:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2054:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2055:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2093:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2094:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2110:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2111:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2403:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2404:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2457:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2458:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2496:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2497:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2513:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2514:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2627:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2628:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2681:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2682:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2720:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2721:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2737:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:2738:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:3111:58: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:3124:61: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4121:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4122:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4175:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4176:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4214:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4215:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4231:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4232:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4346:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4347:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4400:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4401:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4439:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4440:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4456:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4457:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4752:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4753:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4806:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4807:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4845:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4846:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4862:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4863:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4977:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:4978:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5031:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5032:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5070:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5071:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5087:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5088:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5468:58: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5481:61: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5768:48: style: Redundant pointer operation on 'nosplice_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5824:37: style: Redundant pointer operation on 'new' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:5883:39: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:6217:46: style: Redundant pointer operation on 'nosplice_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:6273:37: style: Redundant pointer operation on 'new' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:6332:37: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:6490:63: style: Redundant pointer operation on 'local_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:6563:63: style: Redundant pointer operation on 'local_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/spliceends.c:558:21: style: Parameter 'splice_qpos' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:572:21: style: Parameter 'splice_qpos' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:619:16: style: Variable 'positions' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:1023:29: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:1034:38: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:1045:51: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:1176:73: style: Parameter 'sitep' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:1614:9: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:1627:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:1627:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:2243:15: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:2255:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:2255:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:2870:56: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:3205:16: style: Variable 'positions' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:3523:73: style: Parameter 'sitep' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:3956:9: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:3969:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:3969:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:4589:15: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:4602:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:4602:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/spliceends.c:5220:54: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:5555:68: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:6007:66: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/spliceends.c:1195:36: style: Variable 'novel_nunivdiags' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/spliceends.c:3542:36: style: Variable 'novel_nunivdiags' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/spliceends.c:6143:19: style: Variable 'nunivdiags' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1.c:3379:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1hr-paired.c:1514:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1hr-paired.c:2736:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1hr-paired.c:4479:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1hr-paired.c:7335:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1.c:2782:48: style:inconclusive: Boolean expression 'heap[3]->diagonal==heap[2]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2024-11-20/src/stage1.c:2793:60: style:inconclusive: Boolean expression 'heap[righti]->diagonal==heap[smallesti]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2024-11-20/src/stage1.c:2874:50: style:inconclusive: Boolean expression 'heap[3]->diagonal==heap[2]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2024-11-20/src/stage1.c:2889:62: style:inconclusive: Boolean expression 'heap[righti]->diagonal==heap[smallesti]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2024-11-20/src/stage1.c:3955:13: style: Variable 'trimstart' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1.c:3900:13: note: trimstart is assigned
gmap-2024-11-20/src/stage1.c:3955:13: note: trimstart is overwritten
gmap-2024-11-20/src/stage1.c:3956:11: style: Variable 'trimend' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1.c:3901:11: note: trimend is assigned
gmap-2024-11-20/src/stage1.c:3956:11: note: trimend is overwritten
gmap-2024-11-20/src/stage1.c:4091:16: style: Variable 'maxexons' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1.c:4048:16: note: maxexons is assigned
gmap-2024-11-20/src/stage1.c:4091:16: note: maxexons is overwritten
gmap-2024-11-20/src/stage1.c:1133:29: style: Redundant pointer operation on 'nnew' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:1133:38: style: Redundant pointer operation on 'overflowp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:1142:29: style: Redundant pointer operation on 'nnew' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:1142:38: style: Redundant pointer operation on 'overflowp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:1153:29: style: Redundant pointer operation on 'nnew' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:1153:38: style: Redundant pointer operation on 'overflowp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:1984:26: style: Redundant pointer operation on 'foundpairp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:2032:26: style: Redundant pointer operation on 'foundpairp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1.c:632:35: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:705:50: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:909:35: style: Parameter 'positions0' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:910:18: style: Parameter 'positions1' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:910:60: style: Parameter 'positions2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:1092:8: style: Variable 'npositions' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage1.c:1665:36: style: Parameter 'npositions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:2548:51: style: Parameter 'ndiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:2695:62: style: Parameter 'ndiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:2931:21: style: Variable 'segmentj' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage1.c:3312:55: style: Parameter 'prev' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:3312:66: style: Parameter 'scores' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1.c:1760:8: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1.c:1766:12: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1.c:1801:8: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1.c:1807:12: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1.c:2601:33: style: Variable 'last_diagonal' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-single.c:205:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1hr-single.c:273:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/splice.c:3808:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/splice.c:3809:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/splice.c:4907:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/splice.c:4908:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2024-11-20/src/splice.c:2956:18: style: Condition 'k-1>=0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/splice.c:2950:18: note: Assuming that condition 'k-1>=0' is not redundant
gmap-2024-11-20/src/splice.c:2956:18: note: Condition 'k-1>=0' is always false
gmap-2024-11-20/src/splice.c:6036:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/splice.c:6058:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/splice.c:6036:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/splice.c:6317:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/splice.c:6338:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/splice.c:6317:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/splice.c:3538:19: style: Variable 'best_splice_qpos' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/splice.c:3488:20: note: best_splice_qpos is assigned
gmap-2024-11-20/src/splice.c:3538:19: note: best_splice_qpos is overwritten
gmap-2024-11-20/src/splice.c:4644:19: style: Variable 'best_splice_qpos' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/splice.c:4594:20: note: best_splice_qpos is assigned
gmap-2024-11-20/src/splice.c:4644:19: note: best_splice_qpos is overwritten
gmap-2024-11-20/src/splice.c:1136:24: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:1136:35: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:1138:27: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:1138:41: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:1296:27: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:1296:41: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:1298:24: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:1298:35: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:2827:42: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:2842:40: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:2916:42: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:2928:40: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3049:53: style: Redundant pointer operation on 'nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3049:70: style: Redundant pointer operation on 'nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3049:87: style: Redundant pointer operation on 'ref_nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3049:108: style: Redundant pointer operation on 'ref_nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3067:54: style: Redundant pointer operation on 'nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3067:71: style: Redundant pointer operation on 'nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3067:88: style: Redundant pointer operation on 'ref_nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3067:109: style: Redundant pointer operation on 'ref_nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3139:53: style: Redundant pointer operation on 'nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3139:70: style: Redundant pointer operation on 'nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3139:87: style: Redundant pointer operation on 'ref_nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3139:108: style: Redundant pointer operation on 'ref_nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3157:54: style: Redundant pointer operation on 'nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3157:71: style: Redundant pointer operation on 'nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3157:88: style: Redundant pointer operation on 'ref_nmismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3157:109: style: Redundant pointer operation on 'ref_nmismatches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3833:51: style: Redundant pointer operation on 'univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3833:69: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3833:85: style: Redundant pointer operation on 'ref_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3833:105: style: Redundant pointer operation on 'endpoints' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3833:119: style: Redundant pointer operation on 'junctions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3887:51: style: Redundant pointer operation on 'univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3887:69: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3887:85: style: Redundant pointer operation on 'ref_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3887:105: style: Redundant pointer operation on 'endpoints' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:3887:119: style: Redundant pointer operation on 'junctions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4932:49: style: Redundant pointer operation on 'univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4932:67: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4932:83: style: Redundant pointer operation on 'ref_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4932:103: style: Redundant pointer operation on 'endpoints' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4932:117: style: Redundant pointer operation on 'junctions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4989:49: style: Redundant pointer operation on 'univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4989:67: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4989:83: style: Redundant pointer operation on 'ref_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4989:103: style: Redundant pointer operation on 'endpoints' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:4989:117: style: Redundant pointer operation on 'junctions' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6006:18: style: Redundant pointer operation on 'best_type' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6006:32: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6006:43: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6006:54: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6006:68: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6006:82: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6006:102: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6007:9: style: Redundant pointer operation on 'best_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6007:37: style: Redundant pointer operation on 'best_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6008:9: style: Redundant pointer operation on 'best_ref_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6008:41: style: Redundant pointer operation on 'best_ref_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6287:22: style: Redundant pointer operation on 'best_type' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6287:36: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6287:47: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6287:58: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6287:72: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6287:86: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6287:106: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6288:13: style: Redundant pointer operation on 'best_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6288:41: style: Redundant pointer operation on 'best_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6289:13: style: Redundant pointer operation on 'best_ref_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:6289:45: style: Redundant pointer operation on 'best_ref_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/splice.c:473:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/splice.c:577:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/splice.c:681:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/splice.c:784:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/splice.c:937:23: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:942:24: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1006:13: style: Parameter 'segmentD_types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1006:34: style: Parameter 'segmentA_types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1007:16: style: Parameter 'segmentD_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1007:40: style: Parameter 'segmentA_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1167:10: style: Parameter 'segmentA_types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1167:31: style: Parameter 'segmentD_types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1168:13: style: Parameter 'segmentA_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:1168:37: style: Parameter 'segmentD_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:2113:13: style: Parameter 'segmenti_sites' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:2113:34: style: Parameter 'segmentj_sites' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:2113:55: style: Parameter 'segmenti_types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:2113:76: style: Parameter 'segmentj_types' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:2114:16: style: Parameter 'segmenti_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:2114:40: style: Parameter 'segmentj_probs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/splice.c:3208:35: style: Variable 'middle_univdiagonal' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:3787:16: style: Variable 'trimpos3' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:3805:12: style: Variable 'nindels_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:3806:12: style: Variable 'nindels_j' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:3808:12: style: Variable 'nindels_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:3809:12: style: Variable 'nindels_j' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:4314:35: style: Variable 'middle_univdiagonal' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:4884:16: style: Variable 'trimpos5' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:4904:12: style: Variable 'nindels_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:4905:12: style: Variable 'nindels_j' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:4907:12: style: Variable 'nindels_i' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/splice.c:4908:12: style: Variable 'nindels_j' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr.c:1840:35: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr.c:1840:57: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr.c:1842:35: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr.c:1842:58: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr.c:670:41: style: Variable 'query_lastpos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-single.c:257:25: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:258:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:258:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:259:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:259:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:350:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:372:25: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:386:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:408:25: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:422:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:443:25: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:457:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:477:25: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:512:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:524:53: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:541:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:553:53: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:570:56: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:582:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:599:56: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:611:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:650:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:652:10: style: Redundant pointer operation on 'incomplete_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:652:43: style: Redundant pointer operation on 'incomplete_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:655:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:655:32: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:668:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:670:7: style: Redundant pointer operation on 'incomplete_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:670:44: style: Redundant pointer operation on 'incomplete_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:673:7: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:673:33: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:770:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:791:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:809:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:814:9: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:814:31: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:815:9: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:815:35: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:838:49: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:854:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:859:9: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:859:31: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:860:9: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:860:35: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:881:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:886:5: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:886:27: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:896:30: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:901:9: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:901:35: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:917:14: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:938:14: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:960:14: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:981:14: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1119:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1121:7: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1121:40: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1122:7: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1122:29: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1153:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1155:7: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1155:41: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1156:7: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1156:30: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1224:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1226:10: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1226:43: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1227:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1227:32: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1254:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1256:10: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1256:44: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1257:10: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1257:33: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1320:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1322:10: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1322:43: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1323:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1323:32: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1350:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1352:10: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1352:44: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1353:10: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1353:33: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1468:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1470:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1470:32: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1471:10: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1471:36: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1473:10: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1473:43: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1474:10: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1474:47: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1759:36: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1759:55: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1760:8: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1760:24: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-single.c:1679:7: warning: Uninitialized variables: paths.first, paths.rest [uninitvar]
gmap-2024-11-20/src/stage1hr-single.c:1595:74: note: Assuming condition is false
gmap-2024-11-20/src/stage1hr-single.c:1679:7: note: Uninitialized variables: paths.first, paths.rest
gmap-2024-11-20/src/stage1hr-single.c:304:26: style: Unused variable: unextended_paths [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:730:12: style: Unused variable: trpath [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:738:8: style: Unused variable: partialp [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:742:21: style: Unused variable: unextended_paths [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:1065:24: style: Variable 'sufficient_score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-single.c:1105:24: style: Variable 'any_imperfect_ends_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-single.c:1135:23: style: Variable 'any_imperfect_ends_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-single.c:1169:23: style: Variable 'any_imperfect_ends_p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-single.c:1065:7: style: Variable 'sufficient_score' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-single.c:1517:17: style: Unused variable: new_paths [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:1517:28: style: Unused variable: complete_paths [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:1517:44: style: Unused variable: unextended_paths [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:1517:62: style: Unused variable: p [unusedVariable]
gmap-2024-11-20/src/stage1hr-single.c:1519:8: style: Unused variable: any_imperfect_ends_p [unusedVariable]
gmap-2024-11-20/src/stage2.c:5747:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage2.c:5779:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage2.c:5811:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage2.c:5843:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage2.c:5931:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:2279:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:2612:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:5637:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:5770:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:6415:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:10692:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gapp [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:11807:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage3.c:12344:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gapp [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage2.c:1559:24: style: Condition 'processed==NULL' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage2.c:2491:24: style: Condition 'processed==NULL' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage2.c:658:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/stage2.c:670:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/stage2.c:1139:43: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage2.c:1138:18: note: prevposition is assigned
gmap-2024-11-20/src/stage2.c:1139:43: note: prevposition is overwritten
gmap-2024-11-20/src/stage2.c:1691:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage2.c:1690:20: note: prevposition is assigned
gmap-2024-11-20/src/stage2.c:1691:45: note: prevposition is overwritten
gmap-2024-11-20/src/stage2.c:1715:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage2.c:1714:20: note: prevposition is assigned
gmap-2024-11-20/src/stage2.c:1715:45: note: prevposition is overwritten
gmap-2024-11-20/src/stage2.c:2084:43: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage2.c:2083:18: note: prevposition is assigned
gmap-2024-11-20/src/stage2.c:2084:43: note: prevposition is overwritten
gmap-2024-11-20/src/stage2.c:2625:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage2.c:2624:20: note: prevposition is assigned
gmap-2024-11-20/src/stage2.c:2625:45: note: prevposition is overwritten
gmap-2024-11-20/src/stage2.c:2649:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage2.c:2648:20: note: prevposition is assigned
gmap-2024-11-20/src/stage2.c:2649:45: note: prevposition is overwritten
gmap-2024-11-20/src/stage2.c:4108:25: style: Redundant pointer operation on 'ncells' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage2.c:4129:28: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage2.c:5050:25: style: Redundant pointer operation on 'ncells' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage2.c:403:38: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:429:38: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:645:33: style: Parameter 'minactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:645:54: style: Parameter 'maxactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:1076:28: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:1086:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:1087:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:1471:24: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:1473:50: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:1487:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:1487:29: style: Variable 'adj_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:1488:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:1488:22: style: Variable 'adj_active' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:2023:45: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:2034:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:2035:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:2405:20: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:2407:46: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:2421:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:2421:29: style: Variable 'adj_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:2422:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:2422:22: style: Variable 'adj_active' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage2.c:3112:37: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:3137:37: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:3438:44: style: Parameter 'npositions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:3669:41: style: Parameter 'minactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:3669:62: style: Parameter 'maxactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:4141:15: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:4141:35: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:4315:13: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:4612:37: style: Parameter 'minactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:4612:58: style: Parameter 'maxactive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:5336:10: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:5336:30: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage2.c:6510:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2024-11-20/src/stage2.c:6462:57: note: Assuming condition is false
gmap-2024-11-20/src/stage2.c:6510:18: note: Uninitialized variable: indexsize
gmap-2024-11-20/src/stage2.c:6844:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2024-11-20/src/stage2.c:6798:57: note: Assuming condition is false
gmap-2024-11-20/src/stage2.c:6844:18: note: Uninitialized variable: indexsize
gmap-2024-11-20/src/stage2.c:7005:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2024-11-20/src/stage2.c:6959:57: note: Assuming condition is false
gmap-2024-11-20/src/stage2.c:7005:18: note: Uninitialized variable: indexsize
gmap-2024-11-20/src/stage2.c:7179:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2024-11-20/src/stage2.c:7132:57: note: Assuming condition is false
gmap-2024-11-20/src/stage2.c:7179:18: note: Uninitialized variable: indexsize
gmap-2024-11-20/src/stage2.c:4166:16: style: Variable 'position' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stopwatch.c:76:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCK_MONOTONIC [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stopwatch.c:107:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCK_MONOTONIC [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1hr-paired.c:7148:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1hr-paired.c:7140:10: note: lowp is assigned
gmap-2024-11-20/src/stage1hr-paired.c:7148:10: note: lowp is overwritten
gmap-2024-11-20/src/stage1hr-paired.c:7166:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1hr-paired.c:7159:10: note: lowp is assigned
gmap-2024-11-20/src/stage1hr-paired.c:7166:10: note: lowp is overwritten
gmap-2024-11-20/src/stage1hr-paired.c:7183:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1hr-paired.c:7176:10: note: lowp is assigned
gmap-2024-11-20/src/stage1hr-paired.c:7183:10: note: lowp is overwritten
gmap-2024-11-20/src/stage1hr-paired.c:7204:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1hr-paired.c:7196:10: note: lowp is assigned
gmap-2024-11-20/src/stage1hr-paired.c:7204:10: note: lowp is overwritten
gmap-2024-11-20/src/stage1hr-paired.c:7376:5: style: Variable 'found_score_5' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2024-11-20/src/stage1hr-paired.c:7289:17: note: found_score_5 is assigned 'querylength5' here.
gmap-2024-11-20/src/stage1hr-paired.c:7376:5: note: Variable 'found_score_5' is assigned an expression that holds the same value.
gmap-2024-11-20/src/stage1hr-paired.c:7377:5: style: Variable 'found_score_3' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2024-11-20/src/stage1hr-paired.c:7290:17: note: found_score_3 is assigned 'querylength3' here.
gmap-2024-11-20/src/stage1hr-paired.c:7377:5: note: Variable 'found_score_3' is assigned an expression that holds the same value.
gmap-2024-11-20/src/stage1hr-paired.c:7792:18: style: Variable 'solved_all_p' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage1hr-paired.c:7729:18: note: solved_all_p is assigned
gmap-2024-11-20/src/stage1hr-paired.c:7792:18: note: solved_all_p is overwritten
gmap-2024-11-20/src/stage1hr-paired.c:7338:5: style:inconclusive: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/stage1hr-paired.c:858:34: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:877:34: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:907:34: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:926:34: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:937:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:937:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:937:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:954:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:954:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:954:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:996:36: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1025:34: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1055:36: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1084:34: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1114:36: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1143:34: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1173:36: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1202:34: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1246:47: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1259:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1259:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1259:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1278:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1278:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1278:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1326:47: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1339:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1339:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1339:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1358:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1358:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1358:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1417:19: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1450:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1485:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1628:31: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1681:31: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1985:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:1985:57: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2212:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2212:52: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2237:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2237:52: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2254:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2254:52: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2293:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2293:52: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2318:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2318:52: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2335:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2335:52: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2465:8: style: Redundant pointer operation on 'found_score_L' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2543:8: style: Redundant pointer operation on 'found_score_H' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2611:26: style: Redundant pointer operation on 'completeL_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2611:42: style: Redundant pointer operation on 'completeH_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2611:58: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2612:5: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2623:27: style: Redundant pointer operation on 'completeL_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2623:43: style: Redundant pointer operation on 'completeH_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2623:59: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2624:6: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2666:25: style: Redundant pointer operation on 'querystart' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2666:40: style: Redundant pointer operation on 'queryend' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2667:17: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2667:42: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2668:3: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2668:24: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2669:3: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2669:29: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2670:3: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2670:25: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2684:22: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2684:47: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2685:8: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2685:29: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2686:8: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2686:34: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2687:8: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2687:30: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2705:18: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2705:43: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2706:4: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2706:25: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2707:4: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2707:30: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2708:4: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2708:26: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2794:33: style: Redundant pointer operation on 'last_method_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2804:33: style: Redundant pointer operation on 'last_method_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2900:41: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2900:57: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2901:6: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2901:29: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2901:47: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2902:6: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2929:41: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2929:57: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2930:6: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2930:29: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2930:47: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:2931:6: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3088:35: style: Redundant pointer operation on 'last_method_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3099:35: style: Redundant pointer operation on 'last_method_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3206:43: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3206:59: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3207:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3207:31: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3207:49: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3208:8: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3235:43: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3235:59: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3236:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3236:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3236:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3237:8: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3265:43: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3265:59: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3265:75: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3266:8: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3266:26: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3267:8: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3295:43: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3295:59: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3296:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3296:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3296:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3297:8: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3325:43: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3325:59: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3326:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3326:31: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3326:49: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3327:8: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3355:43: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3355:59: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3356:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3356:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3356:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3357:8: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3629:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:3645:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4024:48: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4024:71: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4024:89: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4060:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4060:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4060:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4083:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4083:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4083:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4106:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4106:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4106:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4129:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4129:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4129:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4522:46: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4580:46: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4611:38: style: Redundant pointer operation on 'npaths5_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4611:58: style: Redundant pointer operation on 'npaths5_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4611:77: style: Redundant pointer operation on 'first_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4611:94: style: Redundant pointer operation on 'second_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4628:38: style: Redundant pointer operation on 'npaths3_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4628:58: style: Redundant pointer operation on 'npaths3_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4628:77: style: Redundant pointer operation on 'first_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4628:94: style: Redundant pointer operation on 'second_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4718:44: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4718:62: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4719:9: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4719:28: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4719:46: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:4719:62: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5008:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5037:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5059:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5059:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5115:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5144:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5166:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5166:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5464:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5484:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5484:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5555:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5575:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5575:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5660:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5680:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5680:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5751:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5771:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5771:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:5982:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6002:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6002:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6073:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6093:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6093:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6179:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6199:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6199:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6270:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6290:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:6290:54: style: Redundant pointer operation on 'unextended_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:7093:11: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:7119:11: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8185:9: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8185:28: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8185:46: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8185:62: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8270:57: style: Redundant pointer operation on 'final_pairtype' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8271:6: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8271:25: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8271:43: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8271:59: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8272:6: style: Redundant pointer operation on 'patharray5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8272:21: style: Redundant pointer operation on 'npaths5_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8272:41: style: Redundant pointer operation on 'npaths5_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8272:60: style: Redundant pointer operation on 'first_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8272:77: style: Redundant pointer operation on 'second_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8273:6: style: Redundant pointer operation on 'patharray3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8273:21: style: Redundant pointer operation on 'npaths3_primary' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8273:41: style: Redundant pointer operation on 'npaths3_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8273:60: style: Redundant pointer operation on 'first_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:8273:77: style: Redundant pointer operation on 'second_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage1hr-paired.c:7220:33: style:inconclusive: Function 'Stage1_paired_read' argument 7 names different: declaration 'nhits5_primary' definition 'npaths5_primary'. [funcArgNamesDifferent]
gmap-2024-11-20/src/stage1hr-paired.h:36:33: note: Function 'Stage1_paired_read' argument 7 names different: declaration 'nhits5_primary' definition 'npaths5_primary'.
gmap-2024-11-20/src/stage1hr-paired.c:7220:33: note: Function 'Stage1_paired_read' argument 7 names different: declaration 'nhits5_primary' definition 'npaths5_primary'.
gmap-2024-11-20/src/stage1hr-paired.c:7220:55: style:inconclusive: Function 'Stage1_paired_read' argument 8 names different: declaration 'nhits5_altloc' definition 'npaths5_altloc'. [funcArgNamesDifferent]
gmap-2024-11-20/src/stage1hr-paired.h:36:54: note: Function 'Stage1_paired_read' argument 8 names different: declaration 'nhits5_altloc' definition 'npaths5_altloc'.
gmap-2024-11-20/src/stage1hr-paired.c:7220:55: note: Function 'Stage1_paired_read' argument 8 names different: declaration 'nhits5_altloc' definition 'npaths5_altloc'.
gmap-2024-11-20/src/stage1hr-paired.c:7221:33: style:inconclusive: Function 'Stage1_paired_read' argument 12 names different: declaration 'nhits3_primary' definition 'npaths3_primary'. [funcArgNamesDifferent]
gmap-2024-11-20/src/stage1hr-paired.h:37:33: note: Function 'Stage1_paired_read' argument 12 names different: declaration 'nhits3_primary' definition 'npaths3_primary'.
gmap-2024-11-20/src/stage1hr-paired.c:7221:33: note: Function 'Stage1_paired_read' argument 12 names different: declaration 'nhits3_primary' definition 'npaths3_primary'.
gmap-2024-11-20/src/stage1hr-paired.c:7221:55: style:inconclusive: Function 'Stage1_paired_read' argument 13 names different: declaration 'nhits3_altloc' definition 'npaths3_altloc'. [funcArgNamesDifferent]
gmap-2024-11-20/src/stage1hr-paired.h:37:54: note: Function 'Stage1_paired_read' argument 13 names different: declaration 'nhits3_altloc' definition 'npaths3_altloc'.
gmap-2024-11-20/src/stage1hr-paired.c:7221:55: note: Function 'Stage1_paired_read' argument 13 names different: declaration 'nhits3_altloc' definition 'npaths3_altloc'.
gmap-2024-11-20/src/stage1hr-paired.c:1766:32: style: Parameter 'completeL_p' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:1766:51: style: Parameter 'completeH_p' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:1767:58: style: Parameter 'indices' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:2002:33: style: Parameter 'completeL_p' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:2002:52: style: Parameter 'completeH_p' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:2003:59: style: Parameter 'indices' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:5193:51: style: Parameter 'exhaustive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:5193:68: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:5210:53: style: Parameter 'exhaustive' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:5210:70: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage1hr-paired.c:4804:10: warning: Uninitialized variables: pathpairarray.mapq_loglik, pathpairarray.mapq_score, pathpairarray.absmq_score, pathpairarray.pairtype, pathpairarray.pair_relationship, pathpairarray.insertlength, pathpairarray.outerlength, pathpairarray.plusp, pathpairarray.transcript_concordant_p, pathpairarray.path5, pathpairarray.path3, pathpairarray.pathL, pathpairarray.pathH, pathpairarray.queryseqL, pathpairarray.queryseqH [uninitvar]
gmap-2024-11-20/src/stage1hr-paired.c:4707:17: note: Assuming condition is false
gmap-2024-11-20/src/stage1hr-paired.c:4747:44: note: Assuming condition is true
gmap-2024-11-20/src/stage1hr-paired.c:4804:10: note: Uninitialized variables: pathpairarray.mapq_loglik, pathpairarray.mapq_score, pathpairarray.absmq_score, pathpairarray.pairtype, pathpairarray.pair_relationship, pathpairarray.insertlength, pathpairarray.outerlength, pathpairarray.plusp, pathpairarray.transcript_concordant_p, pathpairarray.path5, pathpairarray.path3, pathpairarray.pathL, pathpairarray.pathH, pathpairarray.queryseqL, pathpairarray.queryseqH
gmap-2024-11-20/src/stage1hr-paired.c:732:12: style: Unused variable: trpath5 [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:732:21: style: Unused variable: trpath3 [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:737:8: style: Unused variable: partialp [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7148:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7166:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7183:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/support.c:660:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/support.c:749:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/stage1hr-paired.c:7204:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7242:10: style: Unused variable: complete_paths_5 [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7242:28: style: Unused variable: complete_paths_3 [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7242:46: style: Unused variable: pp [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7242:53: style: Unused variable: q [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7274:15: style: Unused variable: univdiagonal_L [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7274:31: style: Unused variable: univdiagonal_H [unusedVariable]
gmap-2024-11-20/src/stage1hr-paired.c:7275:12: style: Unused variable: inner_extension_dist [unusedVariable]
gmap-2024-11-20/src/table.c:66:35: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2024-11-20/src/table.c:79:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/table.c:43:9: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/table.c:44:9: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/table.c:69:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/table.c:243:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/table.c:244:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/table.c:168:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/tableint.c:44:38: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2024-11-20/src/tableint.c:57:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/tableint.c:47:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/tableint.c:182:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableint.c:183:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableint.c:224:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableint.c:225:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableint.c:132:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/tableuint.c:44:39: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2024-11-20/src/support.c:701:7: warning: %u in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
gmap-2024-11-20/src/support.c:708:7: warning: %u in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
gmap-2024-11-20/src/support.c:715:7: warning: %u in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
gmap-2024-11-20/src/support.c:478:10: style: Variable 'chrnum' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/support.c:433:10: note: chrnum is assigned
gmap-2024-11-20/src/support.c:478:10: note: chrnum is overwritten
gmap-2024-11-20/src/tableuint.c:57:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/support.c:478:10: style: Variable 'chrnum' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/support.c:454:9: note: chrnum is assigned
gmap-2024-11-20/src/support.c:478:10: note: chrnum is overwritten
gmap-2024-11-20/src/support.c:659:23: style: Redundant pointer operation on 'low_chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/support.c:666:23: style: Redundant pointer operation on 'high_chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/support.c:617:19: style: Parameter 'last_chr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/support.c:618:20: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/support.c:635:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableuint.c:47:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/tableuint.c:182:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableuint.c:183:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableuint.c:132:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/support.c:807:3: warning: Uninitialized variable: last_chr [uninitvar]
gmap-2024-11-20/src/support.c:746:15: note: Assuming condition is false
gmap-2024-11-20/src/support.c:807:3: note: Uninitialized variable: last_chr
gmap-2024-11-20/src/support.c:478:10: style: Variable 'chrnum' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/support.c:499:9: style: Variable 'chrnum' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/support.c:719:7: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/tableuint8.c:45:39: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2024-11-20/src/tableuint8.c:58:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/tableuint8.c:242:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/tableuint8.c:48:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/tableuint8.c:196:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableuint8.c:197:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/tableuint8.c:146:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/transcript-remap.c:936:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2024-11-20/src/transcript-remap.c:68:35: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:68:57: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:78:56: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:112:36: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:112:58: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:122:57: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:1209:11: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:1209:33: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:1235:12: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:1235:34: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-remap.c:936:10: style: Variable 'path' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/tr-extension-search.c:664:35: style: Condition '(queryoffset=plus_qpos)>=query_lastpos' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/tr-extension-search.c:663:13: note: Assuming that condition 'plus_qpos<query_lastpos' is not redundant
gmap-2024-11-20/src/tr-extension-search.c:664:35: note: Condition '(queryoffset=plus_qpos)>=query_lastpos' is always false
gmap-2024-11-20/src/tr-extension-search.c:709:36: style: Condition '(queryoffset=minus_qpos)>=query_lastpos' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/tr-extension-search.c:663:43: note: Assuming that condition 'minus_qpos<query_lastpos' is not redundant
gmap-2024-11-20/src/tr-extension-search.c:709:36: note: Condition '(queryoffset=minus_qpos)>=query_lastpos' is always false
gmap-2024-11-20/src/tr-extension-search.c:914:35: style: Condition '(queryoffset=plus_qpos)<0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/tr-extension-search.c:913:13: note: Assuming that condition 'plus_qpos>0' is not redundant
gmap-2024-11-20/src/tr-extension-search.c:914:35: note: Condition '(queryoffset=plus_qpos)<0' is always false
gmap-2024-11-20/src/tr-extension-search.c:959:36: style: Condition '(queryoffset=minus_qpos)<0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/tr-extension-search.c:913:31: note: Assuming that condition 'minus_qpos>0' is not redundant
gmap-2024-11-20/src/tr-extension-search.c:959:36: note: Condition '(queryoffset=minus_qpos)<0' is always false
gmap-2024-11-20/src/tr-extension-search.c:172:22: style: Redundant pointer operation on 'set' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:824:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:834:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:851:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:853:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1077:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1087:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1104:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1106:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1370:33: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1370:49: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1370:75: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1380:33: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1380:49: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1380:79: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1596:18: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1597:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1597:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1598:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1598:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1709:18: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1710:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1710:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1711:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1711:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1822:18: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1823:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1823:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1824:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1824:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1883:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1884:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1884:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1885:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1885:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1894:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1895:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1895:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1896:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1896:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1905:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1906:10: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1906:36: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1907:10: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1907:28: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1921:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1922:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1922:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1923:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1923:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1932:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1933:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1933:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1934:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1934:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1943:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1944:10: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1944:36: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1945:10: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:1945:28: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/tr-extension-search.c:250:27: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/tr-extension-search.c:363:27: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcript-velocity.c:273:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/transcript-velocity.c:347:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/transcript.c:887:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/transcript.c:1106:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/transcript.c:644:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2024-11-20/src/transcript.c:643:25: note: outer condition: q!=NULL
gmap-2024-11-20/src/transcript.c:644:11: note: opposite inner condition: q==NULL
gmap-2024-11-20/src/transcript.c:682:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2024-11-20/src/transcript.c:681:25: note: outer condition: r!=NULL
gmap-2024-11-20/src/transcript.c:682:11: note: opposite inner condition: r==NULL
gmap-2024-11-20/src/transcript.c:721:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2024-11-20/src/transcript.c:720:25: note: outer condition: q!=NULL
gmap-2024-11-20/src/transcript.c:721:11: note: opposite inner condition: q==NULL
gmap-2024-11-20/src/transcript.c:760:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2024-11-20/src/transcript.c:759:25: note: outer condition: r!=NULL
gmap-2024-11-20/src/transcript.c:760:11: note: opposite inner condition: r==NULL
gmap-2024-11-20/src/transcript.c:84:34: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcript.c:115:22: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcript-velocity.c:273:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/transcript-velocity.c:347:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/transcriptome.c:134:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/transcriptome.c:105:26: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcriptome.c:105:46: style: Parameter 'genome_fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcriptome.c:106:12: style: Parameter 'transcriptomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcriptome.c:106:39: style: Parameter 'transcriptome_fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:315:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/translation.c:455:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/translation.c:703:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/translation.c:778:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/transcriptome-search.c:431:43: style: Redundant pointer operation on 'n_sense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:435:47: style: Redundant pointer operation on 'n_antisense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:1325:26: style: Redundant pointer operation on 'ndiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:1345:26: style: Redundant pointer operation on 'ndiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:1389:43: style: Redundant pointer operation on 'n_sense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:1396:47: style: Redundant pointer operation on 'n_antisense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:1403:43: style: Redundant pointer operation on 'n_sense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:1406:47: style: Redundant pointer operation on 'n_antisense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/transcriptome-search.c:388:14: style: Variable 'tplus_positions_end5' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/transcriptome-search.c:388:44: style: Variable 'tminus_positions_end5' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/transcriptome-search.c:389:6: style: Variable 'tplus_positions_end3' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/transcriptome-search.c:389:36: style: Variable 'tminus_positions_end3' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/transcriptome-search.c:1236:28: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcriptome-search.c:1259:46: style: Parameter 'all_diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/transcriptome-search.c:390:30: style: Variable 'n_tplus_positions_end5' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/transcriptome-search.c:390:59: style: Variable 'n_tminus_positions_end5' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/transcriptome-search.c:391:28: style: Variable 'n_tplus_positions_end3' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/transcriptome-search.c:391:57: style: Variable 'n_tminus_positions_end3' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trindex.c:192:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/trindex.c:430:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/trindex.c:366:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/trindex.c:327:13: note: Assuming allocation function fails
gmap-2024-11-20/src/trindex.c:327:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2024-11-20/src/trindex.c:366:10: note: Null pointer dereference
gmap-2024-11-20/src/trindex.c:373:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/trindex.c:370:13: note: Assuming allocation function fails
gmap-2024-11-20/src/trindex.c:370:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2024-11-20/src/trindex.c:373:3: note: Null pointer dereference
gmap-2024-11-20/src/trindex.c:374:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/trindex.c:370:13: note: Assuming allocation function fails
gmap-2024-11-20/src/trindex.c:370:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2024-11-20/src/trindex.c:374:10: note: Null pointer dereference
gmap-2024-11-20/src/trindex.c:384:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/trindex.c:381:13: note: Assuming allocation function fails
gmap-2024-11-20/src/trindex.c:381:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2024-11-20/src/trindex.c:384:3: note: Null pointer dereference
gmap-2024-11-20/src/trindex.c:385:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2024-11-20/src/trindex.c:381:13: note: Assuming allocation function fails
gmap-2024-11-20/src/trindex.c:381:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2024-11-20/src/trindex.c:385:10: note: Null pointer dereference
gmap-2024-11-20/src/translation.c:532:7: style: Same expression used in consecutive assignments of 'start0' and 'start1'. [duplicateAssignExpression]
gmap-2024-11-20/src/translation.c:532:34: note: Same expression used in consecutive assignments of 'start0' and 'start1'.
gmap-2024-11-20/src/translation.c:532:7: note: Same expression used in consecutive assignments of 'start0' and 'start1'.
gmap-2024-11-20/src/translation.c:532:34: style: Same expression used in consecutive assignments of 'start1' and 'start2'. [duplicateAssignExpression]
gmap-2024-11-20/src/translation.c:532:61: note: Same expression used in consecutive assignments of 'start1' and 'start2'.
gmap-2024-11-20/src/translation.c:532:34: note: Same expression used in consecutive assignments of 'start1' and 'start2'.
gmap-2024-11-20/src/translation.c:1742:27: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/translation.c:1746:24: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/translation.c:1751:26: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/translation.c:1760:28: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/translation.c:1764:25: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/translation.c:1769:27: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/translation.c:879:24: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:921:24: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:966:55: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:987:48: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:1007:53: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:1028:56: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:1048:49: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:1068:54: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:1427:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:1460:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:1511:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:1544:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:2236:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:2256:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/translation.c:2279:84: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:2326:62: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/translation.c:881:26: style: Variable 'nt2' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:923:26: style: Variable 'nt2' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:1442:10: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:1526:10: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:1996:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:2040:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:2082:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:2124:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:2447:16: style: Variable 'aapos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/translation.c:2470:16: style: Variable 'aapos' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-eval.c:275:33: style:inconclusive: Function 'Trpath_eval_setup' argument 1 names different: declaration 'transcriptome_in' definition 'transcriptomebits_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/trpath-eval.h:26:33: note: Function 'Trpath_eval_setup' argument 1 names different: declaration 'transcriptome_in' definition 'transcriptomebits_in'.
gmap-2024-11-20/src/trpath-eval.c:275:33: note: Function 'Trpath_eval_setup' argument 1 names different: declaration 'transcriptome_in' definition 'transcriptomebits_in'.
gmap-2024-11-20/src/trpath-eval.c:261:38: warning: Uninitialized variable: qend [uninitvar]
gmap-2024-11-20/src/trpath-eval.c:211:91: note: Assuming condition is false
gmap-2024-11-20/src/trpath-eval.c:261:38: note: Uninitialized variable: qend
gmap-2024-11-20/src/trpath-eval.c:61:15: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-eval.c:204:15: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:1741:8: style: Condition '1||(Intlist_head(path->endpoints)==0&&Intlist_last_value(path->endpoints)==querylength)' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/trpath-convert.c:1787:8: style: Condition '1||(Intlist_head(path->endpoints)==0&&Intlist_last_value(path->endpoints)==querylength)' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/trpath-convert.c:1871:8: style: Condition '1||(Intlist_head(path->endpoints)==0&&Intlist_last_value(path->endpoints)==querylength)' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/trpath-convert.c:1915:8: style: Condition '1||(Intlist_head(path->endpoints)==0&&Intlist_last_value(path->endpoints)==querylength)' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/trpath-convert.c:800:41: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:902:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:1550:41: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:1651:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:1729:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:1775:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:1859:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:1903:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-convert.c:63:42: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/trpath-convert.c:430:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:507:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:518:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:563:36: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:1180:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:1257:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:1268:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath-convert.c:1321:36: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/trpath.c:392:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'Trnum_T {aka unsigned int}'. [invalidPrintfArgType_sint]
gmap-2024-11-20/src/trpath.c:106:26: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath.c:123:25: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath.c:146:44: style:inconclusive: Function 'Trpath_new_for_tstart_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'. [funcArgNamesDifferent]
gmap-2024-11-20/src/trpath.h:78:44: note: Function 'Trpath_new_for_tstart_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2024-11-20/src/trpath.c:146:44: note: Function 'Trpath_new_for_tstart_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2024-11-20/src/trpath.c:183:42: style:inconclusive: Function 'Trpath_new_for_tend_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'. [funcArgNamesDifferent]
gmap-2024-11-20/src/trpath.h:85:42: note: Function 'Trpath_new_for_tend_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2024-11-20/src/trpath.c:183:42: note: Function 'Trpath_new_for_tend_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2024-11-20/src/trpath.c:53:13: style: Unused variable: q [unusedVariable]
gmap-2024-11-20/src/trpath.c:316:13: style: Unused variable: q [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:112:11: style: Condition '0&&score>sufficient_score' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/trpath-solve.c:710:13: style: Condition '0&&score>sufficient_score' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/trpath-solve.c:624:9: style: Variable 'tend1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/trpath-solve.c:587:9: note: tend1 is assigned
gmap-2024-11-20/src/trpath-solve.c:624:9: note: tend1 is overwritten
gmap-2024-11-20/src/trpath-solve.c:623:11: style: Variable 'tstart1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/trpath-solve.c:588:11: note: tstart1 is assigned
gmap-2024-11-20/src/trpath-solve.c:623:11: note: tstart1 is overwritten
gmap-2024-11-20/src/trpath-solve.c:628:11: style: Variable 'tstart2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/trpath-solve.c:590:11: note: tstart2 is assigned
gmap-2024-11-20/src/trpath-solve.c:628:11: note: tstart2 is overwritten
gmap-2024-11-20/src/trpath-solve.c:629:9: style: Variable 'tend2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/trpath-solve.c:591:9: note: tend2 is assigned
gmap-2024-11-20/src/trpath-solve.c:629:9: note: tend2 is overwritten
gmap-2024-11-20/src/trpath-solve.c:141:33: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-solve.c:141:49: style: Redundant pointer operation on 'partial_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-solve.c:141:69: style: Redundant pointer operation on 'complete_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-solve.c:942:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/trpath-solve.c:1212:60: style:inconclusive: Function 'Trpath_solve_setup' argument 6 names different: declaration 'index1part_tr' definition 'index1part_tr_in'. [funcArgNamesDifferent]
gmap-2024-11-20/src/trpath-solve.h:75:11: note: Function 'Trpath_solve_setup' argument 6 names different: declaration 'index1part_tr' definition 'index1part_tr_in'.
gmap-2024-11-20/src/trpath-solve.c:1212:60: note: Function 'Trpath_solve_setup' argument 6 names different: declaration 'index1part_tr' definition 'index1part_tr_in'.
gmap-2024-11-20/src/trpath-solve.c:164:7: style: Unused variable: nindels [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:164:16: style: Unused variable: indel_pos [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:165:7: style: Unused variable: nmismatches_i [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:165:22: style: Unused variable: nmismatches_j [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:165:37: style: Unused variable: ref_nmismatches_i [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:165:56: style: Unused variable: ref_nmismatches_j [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:338:7: style: Unused variable: nindels [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:338:16: style: Unused variable: indel_pos [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:339:7: style: Unused variable: nmismatches_i [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:339:22: style: Unused variable: nmismatches_j [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:339:37: style: Unused variable: ref_nmismatches_i [unusedVariable]
gmap-2024-11-20/src/trpath-solve.c:339:56: style: Unused variable: ref_nmismatches_j [unusedVariable]
gmap-2024-11-20/src/uint8list.c:153:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/uint8list.c:171:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/uint8list.c:189:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/uint8list.c:270:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2024-11-20/src/uint8list.c:265:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2024-11-20/src/uint8list.c:267:20: note: Assuming condition is false
gmap-2024-11-20/src/uint8list.c:270:10: note: Null pointer dereference
gmap-2024-11-20/src/uint8list.c:92:23: style:inconclusive: Function 'Uint8list_head_set' argument 1 names different: declaration 'list' definition 'this'. [funcArgNamesDifferent]
gmap-2024-11-20/src/uint8list.h:111:23: note: Function 'Uint8list_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2024-11-20/src/uint8list.c:92:23: note: Function 'Uint8list_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2024-11-20/src/uint8list.c:226:30: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/uint8list.c:241:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2024-11-20/src/uint8tableuint.c:168:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/uint8tableuint.c:214:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2024-11-20/src/uint8tableuint.c:36:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/uint8tableuint.c:186:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/uint8tableuint.c:187:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/uintlist.c:289:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2024-11-20/src/uintlist.c:284:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2024-11-20/src/uintlist.c:286:20: note: Assuming condition is false
gmap-2024-11-20/src/uintlist.c:289:10: note: Null pointer dereference
gmap-2024-11-20/src/uintlist.c:95:22: style:inconclusive: Function 'Uintlist_head_set' argument 1 names different: declaration 'list' definition 'this'. [funcArgNamesDifferent]
gmap-2024-11-20/src/uintlist.h:120:22: note: Function 'Uintlist_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2024-11-20/src/uintlist.c:95:22: note: Function 'Uintlist_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2024-11-20/src/uintlist.c:245:36: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/uintlist.c:260:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2024-11-20/src/stage3.c:6684:19: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2024-11-20/src/stage3.c:6680:19: note: First condition
gmap-2024-11-20/src/stage3.c:6684:19: note: Second condition
gmap-2024-11-20/src/stage3.c:6708:19: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2024-11-20/src/stage3.c:6704:19: note: First condition
gmap-2024-11-20/src/stage3.c:6708:19: note: Second condition
gmap-2024-11-20/src/stage3.c:4013:16: style: Condition '0&&ambig_end_length>0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:4499:16: style: Condition '0&&ambig_end_length>0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:9059:36: style: Condition 'genomejump<=0' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:9057:38: note: Assignment 'genomejump=genomedp3-genomedp5+1', assigned value is greater than 0
gmap-2024-11-20/src/stage3.c:9059:36: note: Condition 'genomejump<=0' is always false
gmap-2024-11-20/src/stage3.c:10376:11: style: Condition '0&&firstpair->querypos!=querydp3_distalgap' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:10610:11: style: Condition '0&&firstpair->querypos!=querydp5_distalgap' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:11412:11: style: Condition '1||(firstpair->querypos==querydp5&&lastpair->querypos==querydp3)' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:17858:23: style: Condition 'watsonp' is always true [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:17808:45: note: Assuming that condition '(watsonp=this_left->watsonp)==1' is not redundant
gmap-2024-11-20/src/stage3.c:17858:23: note: Condition 'watsonp' is always true
gmap-2024-11-20/src/stage3.c:17921:23: style: Condition 'watsonp' is always false [knownConditionTrueFalse]
gmap-2024-11-20/src/stage3.c:17808:45: note: Assuming that condition '(watsonp=this_left->watsonp)==1' is not redundant
gmap-2024-11-20/src/stage3.c:17921:23: note: Condition 'watsonp' is always false
gmap-2024-11-20/src/uinttable.c:34:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/uinttable.c:202:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/uinttable.c:203:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/uintpairtable.c:36:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/stage3.c:3627:11: warning: Either the condition 'pairs!=NULL' is redundant or there is possible null pointer dereference: pairs. [nullPointerRedundantCheck]
gmap-2024-11-20/src/stage3.c:3617:16: note: Assuming that condition 'pairs!=NULL' is not redundant
gmap-2024-11-20/src/stage3.c:3627:11: note: Null pointer dereference
gmap-2024-11-20/src/stage3.c:12418:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/stage3.c:12429:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/stage3.c:12418:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/stage3.c:18180:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2024-11-20/src/stage3.c:18182:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/stage3.c:18180:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2024-11-20/src/uinttableuint.c:34:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2024-11-20/src/uinttableuint.c:184:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/uinttableuint.c:185:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/uinttable_rh.c:80:20: style:inconclusive: Function 'Uinttable_new' argument 1 names different: declaration 'n' definition 'hint'. [funcArgNamesDifferent]
gmap-2024-11-20/src/uinttable_rh.h:14:20: note: Function 'Uinttable_new' argument 1 names different: declaration 'n' definition 'hint'.
gmap-2024-11-20/src/uinttable_rh.c:80:20: note: Function 'Uinttable_new' argument 1 names different: declaration 'n' definition 'hint'.
gmap-2024-11-20/src/stage3.c:1536:5: style: Variable 'pair' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2024-11-20/src/stage3.c:1510:10: note: pair is assigned '(struct Pair_TPair_T)pairs->first' here.
gmap-2024-11-20/src/stage3.c:1536:5: note: Variable 'pair' is assigned an expression that holds the same value.
gmap-2024-11-20/src/stage3.c:10687:13: style: Variable 'start' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage3.c:10670:13: note: start is assigned
gmap-2024-11-20/src/stage3.c:10687:13: note: start is overwritten
gmap-2024-11-20/src/stage3.c:10885:13: style: Variable 'start' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage3.c:10868:13: note: start is assigned
gmap-2024-11-20/src/stage3.c:10885:13: note: start is overwritten
gmap-2024-11-20/src/stage3.c:18190:8: style: Variable 'end1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage3.c:18164:8: note: end1 is assigned
gmap-2024-11-20/src/stage3.c:18190:8: note: end1 is overwritten
gmap-2024-11-20/src/stage3.c:18191:10: style: Variable 'start2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2024-11-20/src/stage3.c:18165:10: note: start2 is assigned
gmap-2024-11-20/src/stage3.c:18191:10: note: start2 is overwritten
gmap-2024-11-20/src/stage3.c:11624:5: style:inconclusive: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/stage3.c:11730:5: style:inconclusive: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2024-11-20/src/stage3.c:909:29: style: Redundant pointer operation on 'matches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:919:29: style: Redundant pointer operation on 'matches2' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:1413:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9081:35: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9261:35: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9277:33: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9277:68: style: Redundant pointer operation on 'incompletep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9510:35: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9531:35: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9664:54: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9832:40: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9889:42: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:9920:44: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10056:40: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10097:39: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10244:52: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10244:75: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10346:56: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10346:73: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10346:96: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10347:14: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10347:35: style: Redundant pointer operation on 'ambig_splicetype' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10358:54: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10358:77: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10478:52: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10478:75: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10580:56: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10580:73: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10580:96: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10581:14: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10581:35: style: Redundant pointer operation on 'ambig_splicetype' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10592:54: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:10592:77: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11491:41: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11500:41: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11508:49: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11508:72: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11524:29: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11613:31: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11613:48: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11614:10: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11614:33: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11614:56: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11624:37: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11624:54: style: Redundant pointer operation on 'chop_exon_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11624:70: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11625:21: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11625:44: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11720:31: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11720:48: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11721:22: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11721:45: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11721:68: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11730:37: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11730:54: style: Redundant pointer operation on 'chop_exon_p' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11730:70: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11731:21: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11731:44: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11821:44: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:11992:39: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12070:37: style: Redundant pointer operation on 'incompletep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12070:53: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12070:76: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12105:27: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12117:42: style: Redundant pointer operation on 'incompletep' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12117:58: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12117:81: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12151:44: style: Redundant pointer operation on 'shiftp' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12151:55: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12151:78: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12197:44: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12243:21: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12243:45: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12244:19: style: Redundant pointer operation on 'nsemicanonical' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:12244:38: style: Redundant pointer operation on 'nnoncanonical' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13806:43: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13806:66: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13806:89: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13855:42: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13855:65: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13855:88: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13952:41: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13952:64: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:13952:87: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:14001:40: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:14001:63: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:14001:86: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:15465:42: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:15465:65: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:15465:88: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:15493:40: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:15493:63: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:15493:86: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16324:41: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16324:60: style: Redundant pointer operation on 'sensedir' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16391:40: style: Redundant pointer operation on 'ambig_end_length_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16391:65: style: Redundant pointer operation on 'ambig_end_length_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16392:7: style: Redundant pointer operation on 'ambig_splicetype_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16392:32: style: Redundant pointer operation on 'ambig_splicetype_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16393:7: style: Redundant pointer operation on 'ambig_prob_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16393:26: style: Redundant pointer operation on 'ambig_prob_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16394:21: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16399:49: style: Redundant pointer operation on 'max_match_length_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16401:31: style: Redundant pointer operation on 'npairs1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16401:43: style: Redundant pointer operation on 'finalpairs1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16404:40: style: Redundant pointer operation on 'matches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16404:53: style: Redundant pointer operation on 'unknowns1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16404:67: style: Redundant pointer operation on 'mismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16405:12: style: Redundant pointer operation on 'qopens1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16405:24: style: Redundant pointer operation on 'qindels1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16405:37: style: Redundant pointer operation on 'topens1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16405:49: style: Redundant pointer operation on 'tindels1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16406:12: style: Redundant pointer operation on 'ncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16406:28: style: Redundant pointer operation on 'nsemicanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16406:48: style: Redundant pointer operation on 'nnoncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16904:41: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16904:60: style: Redundant pointer operation on 'sensedir' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16971:40: style: Redundant pointer operation on 'ambig_end_length_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16971:65: style: Redundant pointer operation on 'ambig_end_length_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16972:7: style: Redundant pointer operation on 'ambig_splicetype_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16972:32: style: Redundant pointer operation on 'ambig_splicetype_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16973:7: style: Redundant pointer operation on 'ambig_prob_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16973:26: style: Redundant pointer operation on 'ambig_prob_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16974:21: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16979:49: style: Redundant pointer operation on 'max_match_length_1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16981:31: style: Redundant pointer operation on 'npairs1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16981:43: style: Redundant pointer operation on 'finalpairs1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16984:40: style: Redundant pointer operation on 'matches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16984:53: style: Redundant pointer operation on 'unknowns1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16984:67: style: Redundant pointer operation on 'mismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16985:12: style: Redundant pointer operation on 'qopens1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16985:24: style: Redundant pointer operation on 'qindels1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16985:37: style: Redundant pointer operation on 'topens1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16985:49: style: Redundant pointer operation on 'tindels1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16986:12: style: Redundant pointer operation on 'ncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16986:28: style: Redundant pointer operation on 'nsemicanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:16986:48: style: Redundant pointer operation on 'nnoncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:17018:25: style: Redundant pointer operation on 'npairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:17018:36: style: Redundant pointer operation on 'pairs' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:17245:19: style: Redundant pointer operation on 'new_left' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:17246:19: style: Redundant pointer operation on 'new_right' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:18042:31: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2024-11-20/src/stage3.c:6361:108: style:inconclusive: Function 'Stage3_print_pslformat_nt' argument 5 names different: declaration 'queryseq' definition 'queryaaseq'. [funcArgNamesDifferent]
gmap-2024-11-20/src/stage3.h:244:108: note: Function 'Stage3_print_pslformat_nt' argument 5 names different: declaration 'queryseq' definition 'queryaaseq'.
gmap-2024-11-20/src/stage3.c:6361:108: note: Function 'Stage3_print_pslformat_nt' argument 5 names different: declaration 'queryseq' definition 'queryaaseq'.
gmap-2024-11-20/src/stage3.c:16426:65: style:inconclusive: Function 'Stage3_compute_one' argument 3 names different: declaration 'pairs1' definition 'finalpairs1'. [funcArgNamesDifferent]
gmap-2024-11-20/src/stage3.h:347:15: note: Function 'Stage3_compute_one' argument 3 names different: declaration 'pairs1' definition 'finalpairs1'.
gmap-2024-11-20/src/stage3.c:16426:65: note: Function 'Stage3_compute_one' argument 3 names different: declaration 'pairs1' definition 'finalpairs1'.
gmap-2024-11-20/src/stage3.c:17031:9: style:inconclusive: Function 'Stage3_mergeable' argument 3 names different: declaration 'exonexonpos' definition 'breakpoint'. [funcArgNamesDifferent]
gmap-2024-11-20/src/stage3.h:373:64: note: Function 'Stage3_mergeable' argument 3 names different: declaration 'exonexonpos' definition 'breakpoint'.
gmap-2024-11-20/src/stage3.c:17031:9: note: Function 'Stage3_mergeable' argument 3 names different: declaration 'exonexonpos' definition 'breakpoint'.
gmap-2024-11-20/src/stage3.c:787:33: style: Parameter 'alias_start' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:787:59: style: Parameter 'alias_end' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:1438:40: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:1438:60: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:1855:72: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:2237:36: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:6647:57: style: Parameter 'map_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:6741:62: style: Parameter 'map_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:11063:14: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:11063:34: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:15417:24: style: Parameter 'cdna_direction' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:17005:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2024-11-20/src/stage3.c:17264:34: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:17460:33: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2024-11-20/src/stage3.c:16817:34: warning: Uninitialized variable: defect_rate_fwd [uninitvar]
gmap-2024-11-20/src/stage3.c:16532:17: note: Assuming condition is true
gmap-2024-11-20/src/stage3.c:16817:34: note: Uninitialized variable: defect_rate_fwd
gmap-2024-11-20/src/stage3.c:16827:34: warning: Uninitialized variable: defect_rate_rev [uninitvar]
gmap-2024-11-20/src/stage3.c:16551:17: note: Assuming condition is true
gmap-2024-11-20/src/stage3.c:16827:34: note: Uninitialized variable: defect_rate_rev
gmap-2024-11-20/src/stage3.c:6668:22: style: Variable 'chrpos1' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:6669:23: style: Variable 'chrpos2' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:6673:23: style: Variable 'chrpos1' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:6674:22: style: Variable 'chrpos2' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9605:30: style: Variable 'acceptable_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9607:30: style: Variable 'acceptable_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9609:30: style: Variable 'acceptable_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9623:9: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9626:9: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9730:46: style: Variable 'left_goodness' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9730:66: style: Variable 'right_goodness' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9984:20: style: Variable 'middle_exonlength' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:9988:20: style: Variable 'middle_exonlength' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:10116:22: style: Variable 'single_goodness' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:10296:19: style: Variable 'protectedp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:10534:19: style: Variable 'protectedp' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:12509:11: style: Variable 'path1' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:12518:11: style: Variable 'path2' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:15426:22: style: Variable 'knownsplice5p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:15426:45: style: Variable 'knownsplice3p' is assigned a value that is never used. [unreadVariable]
gmap-2024-11-20/src/stage3.c:17070:18: style: Variable 'watsonp' is assigned a value that is never used. [unreadVariable]
diff:
head gmap-2024-11-20/src/datadir.c:43:2: error: #error A default value for GMAPDB was not provided to configure.  Please do so, or edit the Makefile [preprocessorErrorDirective]
head gmap-2024-11-20/src/gmap.c:818:16: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
head gmap-2024-11-20/src/gmap.c:818:28: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
head gmap-2024-11-20/src/gsnap.c:900:16: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
head gmap-2024-11-20/src/gsnap.c:900:28: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
head gmap-2024-11-20/src/oligoindex_hr.c:21383:23: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 21381. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:30771:24: note: Assignment 'left_plus_length=0', assigned value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:30779:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:30828:77: note: Calling function 'count_9mers_rev_partial', 6th argument 'enddiscard' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:21381:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:21383:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:21400:26: warning: Shifting 32-bit value by 64 bits is undefined behaviour. See condition at line 21398. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:30771:24: note: Assignment 'left_plus_length=0', assigned value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:30779:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:30828:77: note: Calling function 'count_9mers_rev_partial', 6th argument 'enddiscard' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:21398:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:21400:26: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:21432:23: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 21430. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:31750:24: note: Assignment 'left_plus_length=0', assigned value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:31759:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:31808:109: note: Calling function 'store_9mers_rev_partial', 9th argument 'enddiscard' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:21430:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:21432:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9072:23: warning: Shifting 32-bit value by 4294967250 bits is undefined behaviour. See condition at line 9070. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9070:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9072:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9072:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*9)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9070:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9072:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9072:33: warning: Expression '2*pos-(64-2*9)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9070:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9072:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9089:24: warning: Shifting 32-bit value by 4294967282 bits is undefined behaviour. See condition at line 9087. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9087:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9089:24: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9089:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*9)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9087:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9089:34: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9089:34: warning: Expression '2*pos-(32-2*9)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19393:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9087:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9089:34: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9118:23: warning: Shifting 32-bit value by 4294967250 bits is undefined behaviour. See condition at line 9116. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:20560:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9116:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9118:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9118:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*9)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20560:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9116:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9118:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9118:33: warning: Expression '2*pos-(64-2*9)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20560:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9116:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9118:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9176:23: warning: Shifting 32-bit value by 4294967248 bits is undefined behaviour. See condition at line 9174. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9174:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9176:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9176:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*8)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9174:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9176:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9176:33: warning: Expression '2*pos-(64-2*8)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9174:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9176:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9193:24: warning: Shifting 32-bit value by 4294967280 bits is undefined behaviour. See condition at line 9191. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9191:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9193:24: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9193:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*8)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9191:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9193:34: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9193:34: warning: Expression '2*pos-(32-2*8)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19395:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9191:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9193:34: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9222:23: warning: Shifting 32-bit value by 4294967248 bits is undefined behaviour. See condition at line 9220. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:20562:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9220:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9222:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9222:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*8)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20562:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9220:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9222:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9222:33: warning: Expression '2*pos-(64-2*8)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20562:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9220:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9222:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9280:23: warning: Shifting 32-bit value by 4294967246 bits is undefined behaviour. See condition at line 9278. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9278:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9280:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9280:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*7)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9278:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9280:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9280:33: warning: Expression '2*pos-(64-2*7)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9278:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9280:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9297:24: warning: Shifting 32-bit value by 4294967278 bits is undefined behaviour. See condition at line 9295. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9295:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9297:24: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9297:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*7)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9295:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9297:34: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9297:34: warning: Expression '2*pos-(32-2*7)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19397:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9295:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9297:34: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9326:23: warning: Shifting 32-bit value by 4294967246 bits is undefined behaviour. See condition at line 9324. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:20564:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9324:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9326:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9326:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*7)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20564:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9324:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9326:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9326:33: warning: Expression '2*pos-(64-2*7)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20564:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9324:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9326:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9384:23: warning: Shifting 32-bit value by 4294967244 bits is undefined behaviour. See condition at line 9382. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9382:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9384:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9384:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*6)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9382:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9384:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9384:33: warning: Expression '2*pos-(64-2*6)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9382:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9384:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9401:24: warning: Shifting 32-bit value by 4294967276 bits is undefined behaviour. See condition at line 9399. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9399:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9401:24: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9401:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*6)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9399:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9401:34: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9401:34: warning: Expression '2*pos-(32-2*6)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19399:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9399:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9401:34: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9430:23: warning: Shifting 32-bit value by 4294967244 bits is undefined behaviour. See condition at line 9428. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:20566:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9428:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9430:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9430:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*6)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20566:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9428:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9430:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9430:33: warning: Expression '2*pos-(64-2*6)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20566:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9428:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9430:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9488:23: warning: Shifting 32-bit value by 4294967242 bits is undefined behaviour. See condition at line 9486. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9486:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9488:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9488:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*5)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9486:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9488:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9488:33: warning: Expression '2*pos-(64-2*5)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9486:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9488:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9505:24: warning: Shifting 32-bit value by 4294967274 bits is undefined behaviour. See condition at line 9503. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9503:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9505:24: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9505:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*5)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9503:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9505:34: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9505:34: warning: Expression '2*pos-(32-2*5)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:19401:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9503:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9505:34: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/oligoindex_hr.c:9534:23: warning: Shifting 32-bit value by 4294967242 bits is undefined behaviour. See condition at line 9532. [shiftTooManyBits]
     gmap-2024-11-20/src/oligoindex_hr.c:20568:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9532:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9534:23: note: Shift
head gmap-2024-11-20/src/oligoindex_hr.c:9534:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*5)'. [integerOverflowCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20568:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9532:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9534:33: note: Integer overflow
head gmap-2024-11-20/src/oligoindex_hr.c:9534:33: warning: Expression '2*pos-(64-2*5)' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversionCond]
     gmap-2024-11-20/src/oligoindex_hr.c:20568:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
     gmap-2024-11-20/src/oligoindex_hr.c:9532:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
     gmap-2024-11-20/src/oligoindex_hr.c:9534:33: note: Negative value is converted to an unsigned value
head gmap-2024-11-20/src/stage1hr-single.c:1065:7: style: Variable 'sufficient_score' is assigned a value that is never used. [unreadVariable]


DONE