2025-11-05 06:24
ftp://ftp.de.debian.org/debian/pool/main/g/gmap/gmap_2025-07-31+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 -j4
platform: Linux-6.12.48+deb13-amd64-x86_64-with-glibc2.41
python: 3.13.5
client-version: 1.3.67
compiler: g++ (Debian 14.2.0-19) 14.2.0
cppcheck: head 2.18.0
head-info: 10cdb3d (2025-11-04 16:38:23 +0100)
count: 4298 4280
elapsed-time: 69.9 76.2
head-timing-info:

old-timing-info:

head results:
gmap-2025-07-31/src/access.c:124:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:150:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:186:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:197:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:317:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IPC_STAT [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:374:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:448:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:487:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:518:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:582:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:679:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IPC_CREAT [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/access.c:898:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/atoiindex.c:129:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/atoiindex.c:419:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/atoiindex.c:461:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/atoiindex.c:657:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/atoiindex.c:828:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/atoiindex.c:991:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/atoiindex.c:1187:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/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-2025-07-31/src/access.c:895:30: style: Redundant pointer operation on 'shmid' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/access.c:895:40: style: Redundant pointer operation on 'key' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/access.c:118:25: style: Parameter 'dest_file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:118:42: style: Parameter 'source_file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:145:26: style: Parameter 'file1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:145:39: style: Parameter 'file2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:183:22: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:194:25: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:369:9: style: Variable 'memory' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/access.c:432:26: style: Parameter 'memory' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:471:39: style: Parameter 'memory' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:512:44: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:577:45: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/access.c:402:29: style: Variable 'nattached' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/atoiindex.c:1019:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2025-07-31/src/atoiindex.c:1020:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2025-07-31/src/atoiindex.c:433:23: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/atoiindex.c:433:39: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/atoiindex.c:622:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/atoiindex.c:622:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/atoiindex.c:793:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/atoiindex.c:793:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/atoiindex.c:610:16: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/atoiindex.c:972:9: style: Unused variable: sequence_fp [unusedVariable]
gmap-2025-07-31/src/bigendian.c:31:14: error: Buffer is accessed out of bounds: buf [bufferAccessOutOfBounds]
gmap-2025-07-31/src/bigendian.c:511:32: portability:inconclusive: Casting from double * to unsigned char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
gmap-2025-07-31/src/bigendian.c:535:24: portability:inconclusive: Casting from double * to unsigned char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
gmap-2025-07-31/src/bigendian.c:40:43: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bigendian.c:97:29: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bigendian.c:220:39: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bigendian.c:511:26: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/auxinfo.c:181:19: style:inconclusive: Function 'Auxinfo_append' argument 1 names different: declaration 'new' definition 'first'. [funcArgNamesDifferent]
gmap-2025-07-31/src/auxinfo.h:53:19: note: Function 'Auxinfo_append' argument 1 names different: declaration 'new' definition 'first'.
gmap-2025-07-31/src/auxinfo.c:181:19: note: Function 'Auxinfo_append' argument 1 names different: declaration 'new' definition 'first'.
gmap-2025-07-31/src/auxinfo.c:181:28: style:inconclusive: Function 'Auxinfo_append' argument 2 names different: declaration 'old' definition 'second'. [funcArgNamesDifferent]
gmap-2025-07-31/src/auxinfo.h:53:26: note: Function 'Auxinfo_append' argument 2 names different: declaration 'old' definition 'second'.
gmap-2025-07-31/src/auxinfo.c:181:28: note: Function 'Auxinfo_append' argument 2 names different: declaration 'old' definition 'second'.
gmap-2025-07-31/src/genomebits.h:413:39: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:413:73: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:414:18: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:414:53: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:415:18: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:415:45: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:460:48: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:460:82: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:461:20: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:461:55: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:462:20: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:462:47: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:463:20: style: Parameter 'snp_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:463:48: style: Parameter 'snp_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:463:75: style: Parameter 'snp_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:545:46: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:545:80: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:546:25: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:546:60: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:547:25: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:547:52: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:549:25: style: Parameter 'mask_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1057:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1057:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1058:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1058:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1059:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1059:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1090:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1090:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1091:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1091:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1092:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1092:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1474:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1474:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1475:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1475:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1476:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1476:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1506:36: style: Parameter 'query_high_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1506:70: style: Parameter 'query_low_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1507:22: style: Parameter 'query_flags_shifted' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1507:57: style: Parameter 'ref_high_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1508:22: style: Parameter 'ref_low_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.h:1508:49: style: Parameter 'ref_flags_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-access.c:2122:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitpack64-incr.c:8373:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitpack64-incr.c:8453:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/altsplice.c:81:29: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/altsplice.c:910:11: style:inconclusive: Function 'Altsplice_resolve_qstart' argument 4 names different: declaration 'medial_nmismatches_L' definition 'medial_nmismatches_H'. [funcArgNamesDifferent]
gmap-2025-07-31/src/altsplice.h:142:11: note: Function 'Altsplice_resolve_qstart' argument 4 names different: declaration 'medial_nmismatches_L' definition 'medial_nmismatches_H'.
gmap-2025-07-31/src/altsplice.c:910:11: note: Function 'Altsplice_resolve_qstart' argument 4 names different: declaration 'medial_nmismatches_L' definition 'medial_nmismatches_H'.
gmap-2025-07-31/src/altsplice.c:185:31: style: Parameter 'univdiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:204:32: style: Parameter 'univdiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:227:15: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:228:18: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:282:13: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:283:16: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:336:14: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:337:17: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:513:12: style: Parameter 'distal_support' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:514:15: style: Parameter 'distal_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/altsplice.c:402:23: warning: Uninitialized variable: best_distali [uninitvar]
gmap-2025-07-31/src/altsplice.c:374:67: note: Assuming condition is true
gmap-2025-07-31/src/altsplice.c:402:23: note: Uninitialized variable: best_distali
gmap-2025-07-31/src/altsplice.c:580:23: warning: Uninitialized variable: best_distali [uninitvar]
gmap-2025-07-31/src/altsplice.c:552:67: note: Assuming condition is true
gmap-2025-07-31/src/altsplice.c:580:23: note: Uninitialized variable: best_distali
gmap-2025-07-31/src/altsplice.c:1305:10: style: Variable 'prob' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/altsplice.c:1384:10: style: Variable 'prob' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/bitpack64-write.c:129:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:154:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:4388:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:4439:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:4650:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:4821:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:5377:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:5554:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-read.c:13308:41: style: Parameter 'columnar' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-read.c:14704:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitpack64-read.c:14907:53: style: Parameter 'bitpackpages' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-read.c:15254:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitpack64-read.c:15260:59: style: Variable 'vertical' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitpack64-read.c:15603:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:99:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitvector.c:116:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitvector.c:425:67: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
gmap-2025-07-31/src/bitvector.c:168:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:168:24: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:198:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:290:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:310:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:331:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:356:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitvector.c:385:20: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/block.c:429:46: style: Redundant pointer operation on 'nfwdhits' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/block.c:431:46: style: Redundant pointer operation on 'nrevhits' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/block.c:445:46: style: Redundant pointer operation on 'nfwdhits' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/block.c:447:46: style: Redundant pointer operation on 'nrevhits' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/bitpack64-readtwo.c:14224:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bitpack64-write.c:5623:17: error: Array 'last_block[64]' accessed at index 64, which is out of bounds. [arrayIndexOutOfBounds]
gmap-2025-07-31/src/bitpack64-write.c:5621:15: note: Assuming that condition 'i<=64' is not redundant
gmap-2025-07-31/src/bitpack64-write.c:5623:17: note: Array index out of bounds
gmap-2025-07-31/src/bzip2.c:41:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bzip2.c:98:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bzip2.c:134:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:5395:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5395:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5423:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5423:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5457:5: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5457:5: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5573:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5573:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5602:7: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5602:7: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5644:5: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bitpack64-write.c:5644:5: portability: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'Oligospace_T {aka unsigned int}'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/bytecoding.c:73:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:135:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:190:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:288:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:415:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:654:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:715:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:771:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:854:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:917:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bytecoding.c:986:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bzip2.c:60:3: style:inconclusive: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/bzip2.c:37:7: style: Unused variable: error [unusedVariable]
gmap-2025-07-31/src/bzip2.c:38:9: style: Unused variable: fp [unusedVariable]
gmap-2025-07-31/src/boyer-moore.c:447:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/bitpack64-write.c:110:12: style: Parameter 'horizontal' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:145:13: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4454:56: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4622:37: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4622:53: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4743:45: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4793:46: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4793:62: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4793:78: style: Parameter 'packsizes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:5347:42: style: Parameter 'pagesfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:5347:59: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:5347:75: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:5516:51: style: Parameter 'pagesfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:5516:68: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:5516:84: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:5517:16: style: Parameter 'packsizes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bitpack64-write.c:4134:22: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/bitpack64-write.c:4733:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/bitpack64-write.c:4907:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/bitpack64-write.c:5506:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/bitpack64-write.c:5693:14: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/boyer-moore.c:200:39: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/boyer-moore.c:289:46: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/boyer-moore.c:464:29: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/boyer-moore.c:464:56: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/boyer-moore.c:465:14: style: Parameter 'bad_char_shift' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/boyer-moore.c:207:44: warning: Uninitialized variable: f [uninitvar]
gmap-2025-07-31/src/changepoint.c:25:62: style: Parameter 'matchscores' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/changepoint.c:133:65: style: Parameter 'matchscores' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:66:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:39:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:39:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:66:3: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:70:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:38:19: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:38:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:70:10: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:71:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:39:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:39:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:71:10: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:77:42: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:76:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:76:14: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:77:42: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:78:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:76:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:76:14: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:78:10: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:99:44: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:98:16: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:98:16: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:99:44: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:100:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_bytes [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:98:16: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:98:16: note: Assignment 'fp_bytes=fopen(bytesfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:100:12: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:104:49: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:103:19: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:103:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:104:49: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:105:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:103:19: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:103:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:105:10: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:130:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:107:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:107:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:130:3: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:133:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:107:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:107:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:133:10: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:183:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:156:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:156:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:183:3: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:187:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_exceptions [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:155:19: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:155:19: note: Assignment 'fp_exceptions=fopen(excfile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:187:10: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:188:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_guide [nullPointerOutOfResources]
gmap-2025-07-31/src/bytecoding.c:156:14: note: Assuming allocation function fails
gmap-2025-07-31/src/bytecoding.c:156:14: note: Assignment 'fp_guide=fopen(guidefile,"w")', assigned value is 0
gmap-2025-07-31/src/bytecoding.c:188:10: note: Null pointer dereference
gmap-2025-07-31/src/bytecoding.c:926:78: style:inconclusive: Function 'Bytecoding_lcpchilddc_lcp_next' argument 3 names different: declaration 'lcpchilddc' definition 'bytes'. [funcArgNamesDifferent]
gmap-2025-07-31/src/bytecoding.h:48:20: note: Function 'Bytecoding_lcpchilddc_lcp_next' argument 3 names different: declaration 'lcpchilddc' definition 'bytes'.
gmap-2025-07-31/src/bytecoding.c:926:78: note: Function 'Bytecoding_lcpchilddc_lcp_next' argument 3 names different: declaration 'lcpchilddc' definition 'bytes'.
gmap-2025-07-31/src/bytecoding.c:27:25: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:27:42: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:27:57: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:27:75: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:88:31: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:88:48: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:88:63: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:88:89: style: Parameter 'bytes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:89:11: style: Parameter 'exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:144:41: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:144:56: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:144:74: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:264:36: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:264:53: style: Parameter 'excfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:264:68: style: Parameter 'guidefile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:264:86: style: Parameter 'child' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:265:24: style: Parameter 'discrim_chars' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:265:54: style: Parameter 'lcpbytes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:398:41: style: Parameter 'bytesfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:398:67: style: Parameter 'child_bytes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:398:95: style: Parameter 'discrim_chars' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:398:125: style: Parameter 'lcpbytes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:609:44: style: Parameter 'bytes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:662:51: style: Parameter 'bytes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:662:65: style: Parameter 'guide' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:726:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bytecoding.c:787:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bytecoding.c:799:73: style: Parameter 'guide' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:799:87: style: Parameter 'exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:801:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bytecoding.c:862:75: style: Parameter 'guide' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:862:89: style: Parameter 'exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:864:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bytecoding.c:926:92: style: Parameter 'child_guide' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:927:12: style: Parameter 'child_exceptions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/bytecoding.c:930:18: style: Variable 'block' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/bytecoding.c:360:17: style: Variable 'bytes_ptr' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/bytecoding.c:446:17: style: Variable 'bytes_ptr' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/chrom.c:133:21: style:inconclusive: Redundant condition: The condition '*p != '\0'' is redundant since '*p >= '0'' is sufficient. [redundantCondition]
gmap-2025-07-31/src/chrom.c:73:56: style:inconclusive: Function 'Chrom_altlocp' argument 2 names different: declaration 'alt_scaffold_stop' definition 'alt_scaffold_end'. [funcArgNamesDifferent]
gmap-2025-07-31/src/chrom.h:20:56: note: Function 'Chrom_altlocp' argument 2 names different: declaration 'alt_scaffold_stop' definition 'alt_scaffold_end'.
gmap-2025-07-31/src/chrom.c:73:56: note: Function 'Chrom_altlocp' argument 2 names different: declaration 'alt_scaffold_stop' definition 'alt_scaffold_end'.
gmap-2025-07-31/src/chrom.c:93:40: style: Parameter 'mitochondrial_string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/chrom.c:97:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/chrom.c:373:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/cmetindex.c:129:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/cmetindex.c:559:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/cmetindex.c:601:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/cmetindex.c:797:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/cmetindex.c:968:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/cmetindex.c:1131:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/cmetindex.c:1327:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/compress-write.c:107:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/compress-write.c:270:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/compress-write.c:322:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/compress-write.c:544:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/compress-write.c:831:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/cmetindex.c:1159:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2025-07-31/src/cmetindex.c:1160:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2025-07-31/src/cmetindex.c:573:23: style: Parameter 'ptrsfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/cmetindex.c:573:39: style: Parameter 'compfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/cmetindex.c:762:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/cmetindex.c:762:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/cmetindex.c:933:12: style: Parameter 'new_positions_high_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/cmetindex.c:933:47: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/cmetindex.c:750:16: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/cmetindex.c:1112:9: style: Unused variable: sequence_fp [unusedVariable]
gmap-2025-07-31/src/compress-write.c:115:39: style: Checking if unsigned expression 'fread(&high,sizeof(unsigned int),1,sequence_fp)' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/compress-write.c:116:31: style: Checking if unsigned expression 'fread(&low,sizeof(unsigned int),1,sequence_fp)' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/compress-write.c:117:33: style: Checking if unsigned expression 'fread(&flags,sizeof(unsigned int),1,sequence_fp)' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/compress-write.c:239:54: style: Parameter 'Buffer' can be declared as const array [constParameter]
gmap-2025-07-31/src/compress-write.c:292:69: style: Parameter 'Buffer' can be declared as const array [constParameter]
gmap-2025-07-31/src/compress-write.c:539:16: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress-write.c:780:44: style: Parameter 'genomecomp' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/compress-write.c:807:9: style: Variable 'file' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress-write.c:974:37: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 990. [shiftTooManyBits]
gmap-2025-07-31/src/compress-write.c:990:17: note: Assuming that condition 'shift==0' is not redundant
gmap-2025-07-31/src/compress-write.c:982:33: note: Assignment to 'shift=32-current_pos'
gmap-2025-07-31/src/compress-write.c:974:37: note: Shift
gmap-2025-07-31/src/compress-write.c:1001:28: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 961. [shiftTooManyBits]
gmap-2025-07-31/src/compress-write.c:961:23: note: Assuming that condition 'current_pos==0' is not redundant
gmap-2025-07-31/src/compress-write.c:982:33: note: Assignment 'shift=32-current_pos', assigned value is 32
gmap-2025-07-31/src/compress-write.c:1001:28: note: Shift
gmap-2025-07-31/src/compress-write.c:1004:36: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 961. [shiftTooManyBits]
gmap-2025-07-31/src/compress-write.c:961:23: note: Assuming that condition 'current_pos==0' is not redundant
gmap-2025-07-31/src/compress-write.c:982:33: note: Assignment 'shift=32-current_pos', assigned value is 32
gmap-2025-07-31/src/compress-write.c:1004:36: note: Shift
gmap-2025-07-31/src/compress-write.c:813:21: style: Variable 'buffer_high' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/compress-write.c:813:37: style: Variable 'buffer_low' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/compress-write.c:815:76: style: Variable 'buffer_flags' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/compress.c:163:17: style: Variable 'high_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:163:31: style: Variable 'low_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:163:44: style: Variable 'flags_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:307:17: style: Variable 'high_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:307:31: style: Variable 'low_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:307:44: style: Variable 'flags_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:343:17: style: Variable 'high_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:343:31: style: Variable 'low_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:343:44: style: Variable 'flags_blocks' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/compress.c:389:25: style: Parameter 'gbuffer' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/compress.c:533:25: style: Parameter 'gbuffer' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/compress.c:395:18: style: Variable 'in_counter' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/compress.c:539:18: style: Variable 'in_counter' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/cpuid.c:22:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/datadir.c:42:0: error: #error A default value for GMAPDB was not provided to configure.  Please do so, or edit the Makefile [preprocessorErrorDirective]
gmap-2025-07-31/src/datadir.c:42:2: error: #error A default value for GMAPDB was not provided to configure.  Please do so, or edit the Makefile [preprocessorErrorDirective]
gmap-2025-07-31/src/chimera.c:483:48: style: Parameter 'circularp' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/diag.c:75:13: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/diag.c:322:48: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/diag.c:322:68: style: Parameter 'genomicseg_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/doublelist.c:18:33: style:inconclusive: Function 'Doublelist_push' argument 2 names different: declaration 'index' definition 'elt'. [funcArgNamesDifferent]
gmap-2025-07-31/src/doublelist.h:7:42: note: Function 'Doublelist_push' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2025-07-31/src/doublelist.c:18:33: note: Function 'Doublelist_push' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2025-07-31/src/doublelist.c:27:33: style:inconclusive: Function 'Doublelist_pop' argument 2 names different: declaration 'index' definition 'elt'. [funcArgNamesDifferent]
gmap-2025-07-31/src/doublelist.h:8:42: note: Function 'Doublelist_pop' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2025-07-31/src/doublelist.c:27:33: note: Function 'Doublelist_pop' argument 2 names different: declaration 'index' definition 'elt'.
gmap-2025-07-31/src/doublelist.c:166:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/doublelist.c:182:32: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/concordance.c:160:26: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:175:26: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:190:30: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:205:30: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:469:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:469:57: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:469:75: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:492:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:492:57: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:492:75: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:515:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:515:57: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:515:75: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/concordance.c:545:56: style:inconclusive: Function 'Concordance_setup' argument 7 names different: declaration 'two_pass_p' definition 'two_pass_p_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/concordance.h:58:56: note: Function 'Concordance_setup' argument 7 names different: declaration 'two_pass_p' definition 'two_pass_p_in'.
gmap-2025-07-31/src/concordance.c:545:56: note: Function 'Concordance_setup' argument 7 names different: declaration 'two_pass_p' definition 'two_pass_p_in'.
gmap-2025-07-31/src/dynprog.c:211:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog.c:1170:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_cdna.c:97:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_cdna.c:1226:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_cdna.c:1275:39: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_cdna.c:786:43: style:inconclusive: Function 'Dynprog_cdna_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_cdna.h:17:43: note: Function 'Dynprog_cdna_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_cdna.c:786:43: note: Function 'Dynprog_cdna_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_cdna.c:1220:14: style: Variable 'finalscore' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/dynprog_end.c:1540:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_end.c:2141:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_end.c:2542:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_end.c:2595:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_end.c:2643:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_end.c:2697:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_genome.c:2912:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_end.c:1571:62: style: Condition '*traceback_score<=0' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/dynprog_end.c:1557:22: note: Assignment '*traceback_score=0', assigned value is 0
gmap-2025-07-31/src/dynprog_end.c:1571:62: note: Condition '*traceback_score<=0' is always true
gmap-2025-07-31/src/dynprog_end.c:2170:62: style: Condition '*traceback_score<=0' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/dynprog_end.c:2157:22: note: Assignment '*traceback_score=0', assigned value is 0
gmap-2025-07-31/src/dynprog_end.c:2170:62: note: Condition '*traceback_score<=0' is always true
gmap-2025-07-31/src/dynprog_end.c:2828:43: style: Condition 'glength>0' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/dynprog_end.c:2788:15: note: Assuming that condition 'glength<=0' is not redundant
gmap-2025-07-31/src/dynprog_end.c:2828:43: note: Condition 'glength>0' is always true
gmap-2025-07-31/src/dynprog_end.c:3090:43: style: Condition 'glength>0' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/dynprog_end.c:3049:15: note: Assuming that condition 'glength<=0' is not redundant
gmap-2025-07-31/src/dynprog_end.c:3090:43: note: Condition 'glength>0' is always true
gmap-2025-07-31/src/dynprog_end.c:1561:35: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1561:55: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1561:68: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1612:40: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1612:60: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1612:73: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1612:89: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1612:100: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1880:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1880:58: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1880:71: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1880:87: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1880:98: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1890:39: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1890:59: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1890:72: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1890:88: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1890:99: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2161:35: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2161:55: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2161:68: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2209:40: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2209:60: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2209:73: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2209:89: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2209:100: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2461:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2461:58: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2461:71: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2461:87: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2461:98: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2470:39: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2470:59: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2470:72: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2470:88: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2470:99: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2803:33: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2803:50: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2803:70: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2803:83: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2804:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2804:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2914:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2914:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2914:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2915:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2915:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2915:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2915:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2919:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2932:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2932:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2932:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2933:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2933:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2933:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2933:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2937:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2967:37: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2967:54: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2967:74: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2967:87: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2968:9: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:2968:20: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3065:33: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3065:50: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3065:70: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3065:83: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3066:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3066:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3176:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3176:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3176:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3177:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3177:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3177:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3177:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3181:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3194:11: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3194:31: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3194:44: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3195:11: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3195:22: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3195:34: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3195:51: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3199:29: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3229:37: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3229:54: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3229:74: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3229:87: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3230:9: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:3230:20: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_end.c:1293:43: style:inconclusive: Function 'Dynprog_end5_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:25:43: note: Function 'Dynprog_end5_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:1293:43: note: Function 'Dynprog_end5_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:1295:11: style:inconclusive: Function 'Dynprog_end5_gap' argument 8 names different: declaration 'revsequence1' definition 'rev_rsequence'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:27:11: note: Function 'Dynprog_end5_gap' argument 8 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2025-07-31/src/dynprog_end.c:1295:11: note: Function 'Dynprog_end5_gap' argument 8 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2025-07-31/src/dynprog_end.c:1295:32: style:inconclusive: Function 'Dynprog_end5_gap' argument 9 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:27:31: note: Function 'Dynprog_end5_gap' argument 9 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:1295:32: note: Function 'Dynprog_end5_gap' argument 9 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:1296:9: style:inconclusive: Function 'Dynprog_end5_gap' argument 10 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:28:9: note: Function 'Dynprog_end5_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:1296:9: note: Function 'Dynprog_end5_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:1296:22: style:inconclusive: Function 'Dynprog_end5_gap' argument 11 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:28:22: note: Function 'Dynprog_end5_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:1296:22: note: Function 'Dynprog_end5_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:1296:35: style:inconclusive: Function 'Dynprog_end5_gap' argument 12 names different: declaration 'revoffset1' definition 'rev_roffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:28:35: note: Function 'Dynprog_end5_gap' argument 12 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2025-07-31/src/dynprog_end.c:1296:35: note: Function 'Dynprog_end5_gap' argument 12 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2025-07-31/src/dynprog_end.c:1296:52: style:inconclusive: Function 'Dynprog_end5_gap' argument 13 names different: declaration 'revoffset2' definition 'rev_goffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:28:51: note: Function 'Dynprog_end5_gap' argument 13 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2025-07-31/src/dynprog_end.c:1296:52: note: Function 'Dynprog_end5_gap' argument 13 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2025-07-31/src/dynprog_end.c:1652:54: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:36:54: note: Function 'Dynprog_end5_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:1652:54: note: Function 'Dynprog_end5_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:1656:13: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:40:13: note: Function 'Dynprog_end5_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:1656:13: note: Function 'Dynprog_end5_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:1656:26: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:40:26: note: Function 'Dynprog_end5_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:1656:26: note: Function 'Dynprog_end5_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:1656:39: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:40:39: note: Function 'Dynprog_end5_splicejunction' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2025-07-31/src/dynprog_end.c:1656:39: note: Function 'Dynprog_end5_splicejunction' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2025-07-31/src/dynprog_end.c:1656:56: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 16 names different: declaration 'revoffset2_anchor' definition 'rev_goffset_anchor'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:40:55: note: Function 'Dynprog_end5_splicejunction' argument 16 names different: declaration 'revoffset2_anchor' definition 'rev_goffset_anchor'.
gmap-2025-07-31/src/dynprog_end.c:1656:56: note: Function 'Dynprog_end5_splicejunction' argument 16 names different: declaration 'revoffset2_anchor' definition 'rev_goffset_anchor'.
gmap-2025-07-31/src/dynprog_end.c:1656:80: style:inconclusive: Function 'Dynprog_end5_splicejunction' argument 17 names different: declaration 'revoffset2_far' definition 'rev_goffset_far'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:40:78: note: Function 'Dynprog_end5_splicejunction' argument 17 names different: declaration 'revoffset2_far' definition 'rev_goffset_far'.
gmap-2025-07-31/src/dynprog_end.c:1656:80: note: Function 'Dynprog_end5_splicejunction' argument 17 names different: declaration 'revoffset2_far' definition 'rev_goffset_far'.
gmap-2025-07-31/src/dynprog_end.c:1923:43: style:inconclusive: Function 'Dynprog_end3_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:47:43: note: Function 'Dynprog_end3_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:1923:43: note: Function 'Dynprog_end3_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:1925:11: style:inconclusive: Function 'Dynprog_end3_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:49:11: note: Function 'Dynprog_end3_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2025-07-31/src/dynprog_end.c:1925:11: note: Function 'Dynprog_end3_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2025-07-31/src/dynprog_end.c:1925:28: style:inconclusive: Function 'Dynprog_end3_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:49:28: note: Function 'Dynprog_end3_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:1925:28: note: Function 'Dynprog_end3_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:1926:9: style:inconclusive: Function 'Dynprog_end3_gap' argument 10 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:50:9: note: Function 'Dynprog_end3_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:1926:9: note: Function 'Dynprog_end3_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:1926:22: style:inconclusive: Function 'Dynprog_end3_gap' argument 11 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:50:22: note: Function 'Dynprog_end3_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:1926:22: note: Function 'Dynprog_end3_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:1926:35: style:inconclusive: Function 'Dynprog_end3_gap' argument 12 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:50:35: note: Function 'Dynprog_end3_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_end.c:1926:35: note: Function 'Dynprog_end3_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_end.c:1926:48: style:inconclusive: Function 'Dynprog_end3_gap' argument 13 names different: declaration 'offset2' definition 'goffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:50:48: note: Function 'Dynprog_end3_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2025-07-31/src/dynprog_end.c:1926:48: note: Function 'Dynprog_end3_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2025-07-31/src/dynprog_end.c:2248:54: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:58:54: note: Function 'Dynprog_end3_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:2248:54: note: Function 'Dynprog_end3_splicejunction' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:2252:13: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:62:13: note: Function 'Dynprog_end3_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:2252:13: note: Function 'Dynprog_end3_splicejunction' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:2252:26: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:62:26: note: Function 'Dynprog_end3_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:2252:26: note: Function 'Dynprog_end3_splicejunction' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:2252:39: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 15 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:62:39: note: Function 'Dynprog_end3_splicejunction' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_end.c:2252:39: note: Function 'Dynprog_end3_splicejunction' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_end.c:2252:52: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 16 names different: declaration 'offset2_anchor' definition 'goffset_anchor'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:62:52: note: Function 'Dynprog_end3_splicejunction' argument 16 names different: declaration 'offset2_anchor' definition 'goffset_anchor'.
gmap-2025-07-31/src/dynprog_end.c:2252:52: note: Function 'Dynprog_end3_splicejunction' argument 16 names different: declaration 'offset2_anchor' definition 'goffset_anchor'.
gmap-2025-07-31/src/dynprog_end.c:2252:72: style:inconclusive: Function 'Dynprog_end3_splicejunction' argument 17 names different: declaration 'offset2_far' definition 'goffset_far'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:62:72: note: Function 'Dynprog_end3_splicejunction' argument 17 names different: declaration 'offset2_far' definition 'goffset_far'.
gmap-2025-07-31/src/dynprog_end.c:2252:72: note: Function 'Dynprog_end3_splicejunction' argument 17 names different: declaration 'offset2_far' definition 'goffset_far'.
gmap-2025-07-31/src/dynprog_end.c:2747:65: style:inconclusive: Function 'Dynprog_end5_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:90:65: note: Function 'Dynprog_end5_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:2747:65: note: Function 'Dynprog_end5_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:2750:13: style:inconclusive: Function 'Dynprog_end5_known' argument 11 names different: declaration 'revsequence1' definition 'rev_rsequence'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:93:13: note: Function 'Dynprog_end5_known' argument 11 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2025-07-31/src/dynprog_end.c:2750:13: note: Function 'Dynprog_end5_known' argument 11 names different: declaration 'revsequence1' definition 'rev_rsequence'.
gmap-2025-07-31/src/dynprog_end.c:2750:34: style:inconclusive: Function 'Dynprog_end5_known' argument 12 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:93:33: note: Function 'Dynprog_end5_known' argument 12 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:2750:34: note: Function 'Dynprog_end5_known' argument 12 names different: declaration 'revsequenceuc1' definition 'rev_rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:2751:11: style:inconclusive: Function 'Dynprog_end5_known' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:94:11: note: Function 'Dynprog_end5_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:2751:11: note: Function 'Dynprog_end5_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:2751:24: style:inconclusive: Function 'Dynprog_end5_known' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:94:24: note: Function 'Dynprog_end5_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:2751:24: note: Function 'Dynprog_end5_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:2751:37: style:inconclusive: Function 'Dynprog_end5_known' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:94:37: note: Function 'Dynprog_end5_known' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2025-07-31/src/dynprog_end.c:2751:37: note: Function 'Dynprog_end5_known' argument 15 names different: declaration 'revoffset1' definition 'rev_roffset'.
gmap-2025-07-31/src/dynprog_end.c:2751:54: style:inconclusive: Function 'Dynprog_end5_known' argument 16 names different: declaration 'revoffset2' definition 'rev_goffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:94:53: note: Function 'Dynprog_end5_known' argument 16 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2025-07-31/src/dynprog_end.c:2751:54: note: Function 'Dynprog_end5_known' argument 16 names different: declaration 'revoffset2' definition 'rev_goffset'.
gmap-2025-07-31/src/dynprog_end.c:3008:65: style:inconclusive: Function 'Dynprog_end3_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:107:65: note: Function 'Dynprog_end3_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:3008:65: note: Function 'Dynprog_end3_known' argument 3 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_end.c:3011:13: style:inconclusive: Function 'Dynprog_end3_known' argument 11 names different: declaration 'sequence1' definition 'rsequence'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:110:13: note: Function 'Dynprog_end3_known' argument 11 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2025-07-31/src/dynprog_end.c:3011:13: note: Function 'Dynprog_end3_known' argument 11 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2025-07-31/src/dynprog_end.c:3011:30: style:inconclusive: Function 'Dynprog_end3_known' argument 12 names different: declaration 'sequenceuc1' definition 'rsequenceuc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:110:30: note: Function 'Dynprog_end3_known' argument 12 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:3011:30: note: Function 'Dynprog_end3_known' argument 12 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2025-07-31/src/dynprog_end.c:3012:11: style:inconclusive: Function 'Dynprog_end3_known' argument 13 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:111:11: note: Function 'Dynprog_end3_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:3012:11: note: Function 'Dynprog_end3_known' argument 13 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_end.c:3012:24: style:inconclusive: Function 'Dynprog_end3_known' argument 14 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:111:24: note: Function 'Dynprog_end3_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:3012:24: note: Function 'Dynprog_end3_known' argument 14 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_end.c:3012:37: style:inconclusive: Function 'Dynprog_end3_known' argument 15 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:111:37: note: Function 'Dynprog_end3_known' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_end.c:3012:37: note: Function 'Dynprog_end3_known' argument 15 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_end.c:3012:50: style:inconclusive: Function 'Dynprog_end3_known' argument 16 names different: declaration 'offset2' definition 'goffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_end.h:111:50: note: Function 'Dynprog_end3_known' argument 16 names different: declaration 'offset2' definition 'goffset'.
gmap-2025-07-31/src/dynprog_end.c:3012:50: note: Function 'Dynprog_end3_known' argument 16 names different: declaration 'offset2' definition 'goffset'.
gmap-2025-07-31/src/dynprog_end.c:649:25: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_end.c:649:42: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_end.c:650:11: style: Parameter 'gsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_end.c:650:28: style: Parameter 'gsequence_alt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_end.c:1139:57: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_end.c:1140:36: style: Parameter 'genomesequencealt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_end.c:2721:50: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_end.c:2873:16: style: Variable 'jstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/dynprog_end.c:3135:16: style: Variable 'jstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/dynprog.c:175:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog.c:1797:47: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog.c:1797:66: style: Parameter 'gsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog.c:1797:83: style: Parameter 'gsequence_alt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:233:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/ef64.c:51:21: style: Parameter 'bits' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/ef64.c:144:37: style: Parameter 'repetitive_oligos' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/ef64.c:393:52: style: Parameter 'endpoints' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/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-2025-07-31/src/ef64.c:185:19: warning: Uninitialized variable: oligo [uninitvar]
gmap-2025-07-31/src/ef64.c:177:17: note: Assuming condition is false
gmap-2025-07-31/src/ef64.c:185:19: note: Uninitialized variable: oligo
gmap-2025-07-31/src/except.c:124:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/dynprog_genome.c:2737:5: style: Variable 'cL' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2025-07-31/src/dynprog_genome.c:2681:8: note: cL is assigned 'rL' here.
gmap-2025-07-31/src/dynprog_genome.c:2737:5: note: Variable 'cL' is assigned an expression that holds the same value.
gmap-2025-07-31/src/dynprog_genome.c:2945:49: style: Redundant pointer operation on 'bestrL' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2945:60: style: Redundant pointer operation on 'bestrR' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2945:71: style: Redundant pointer operation on 'bestcL' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2945:82: style: Redundant pointer operation on 'bestcR' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2945:93: style: Redundant pointer operation on 'best_introntype' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2952:47: style: Redundant pointer operation on 'bestrL' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2952:58: style: Redundant pointer operation on 'bestrR' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2952:69: style: Redundant pointer operation on 'bestcL' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2952:80: style: Redundant pointer operation on 'bestcR' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2985:26: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:2985:40: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3170:26: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3170:40: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3479:34: style: Redundant pointer operation on 'introntype' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3479:49: style: Redundant pointer operation on 'new_leftgenomepos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3479:71: style: Redundant pointer operation on 'new_rightgenomepos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3480:6: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3480:20: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3480:35: style: Redundant pointer operation on 'exonhead' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3481:6: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3481:26: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3481:39: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3817:11: style: Redundant pointer operation on 'introntype' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3817:26: style: Redundant pointer operation on 'left_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3817:40: style: Redundant pointer operation on 'right_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3841:40: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3841:60: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3841:73: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3841:89: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3841:100: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3870:41: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3870:61: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3870:74: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3870:90: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:3870:101: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_genome.c:333:14: style: Parameter 'left_known' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:333:31: style: Parameter 'right_known' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2369:10: style: Parameter 'left_known' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2369:27: style: Parameter 'right_known' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2471:16: style: Parameter 'gsequenceL' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2471:34: style: Parameter 'gsequenceL_alt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2471:56: style: Parameter 'rev_gsequenceR' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2471:78: style: Parameter 'rev_gsequenceR_alt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2472:47: style: Parameter 'left_known' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2472:64: style: Parameter 'right_known' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:2490:8: style: Variable 'intron_score_array' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/dynprog_genome.c:3008:12: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3008:29: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3008:48: style: Parameter 'rev_rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3008:69: style: Parameter 'rev_rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3009:12: style: Parameter 'gsequenceL' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3009:30: style: Parameter 'gsequenceL_alt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3009:52: style: Parameter 'rev_gsequenceR' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3009:74: style: Parameter 'rev_gsequenceR_alt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_genome.c:3029:8: style: Variable 'intron_score_array' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/dynprog_genome.c:3408:29: style: Variable 'rev_roffset' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/dynprog_genome.c:3426:29: style: Variable 'rev_roffset' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/dynprog_genome.c:3816:19: style: Variable 'finalscore' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/dynprog_single.c:142:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:578:36: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:578:56: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:578:69: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:643:38: style: Redundant pointer operation on 'traceback_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:643:58: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:643:71: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:643:87: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:643:98: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/dynprog_single.c:428:45: style:inconclusive: Function 'Dynprog_single_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_single.h:22:45: note: Function 'Dynprog_single_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_single.c:428:45: note: Function 'Dynprog_single_gap' argument 2 names different: declaration 'finalscore' definition 'traceback_score'.
gmap-2025-07-31/src/dynprog_single.c:429:24: style:inconclusive: Function 'Dynprog_single_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_single.h:24:24: note: Function 'Dynprog_single_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2025-07-31/src/dynprog_single.c:429:24: note: Function 'Dynprog_single_gap' argument 8 names different: declaration 'sequence1' definition 'rsequence'.
gmap-2025-07-31/src/dynprog_single.c:429:41: style:inconclusive: Function 'Dynprog_single_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_single.h:24:41: note: Function 'Dynprog_single_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2025-07-31/src/dynprog_single.c:429:41: note: Function 'Dynprog_single_gap' argument 9 names different: declaration 'sequenceuc1' definition 'rsequenceuc'.
gmap-2025-07-31/src/dynprog_single.c:430:11: style:inconclusive: Function 'Dynprog_single_gap' argument 10 names different: declaration 'length1' definition 'rlength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_single.h:25:11: note: Function 'Dynprog_single_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_single.c:430:11: note: Function 'Dynprog_single_gap' argument 10 names different: declaration 'length1' definition 'rlength'.
gmap-2025-07-31/src/dynprog_single.c:430:24: style:inconclusive: Function 'Dynprog_single_gap' argument 11 names different: declaration 'length2' definition 'glength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_single.h:25:24: note: Function 'Dynprog_single_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_single.c:430:24: note: Function 'Dynprog_single_gap' argument 11 names different: declaration 'length2' definition 'glength'.
gmap-2025-07-31/src/dynprog_single.c:430:37: style:inconclusive: Function 'Dynprog_single_gap' argument 12 names different: declaration 'offset1' definition 'roffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_single.h:25:37: note: Function 'Dynprog_single_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_single.c:430:37: note: Function 'Dynprog_single_gap' argument 12 names different: declaration 'offset1' definition 'roffset'.
gmap-2025-07-31/src/dynprog_single.c:430:50: style:inconclusive: Function 'Dynprog_single_gap' argument 13 names different: declaration 'offset2' definition 'goffset'. [funcArgNamesDifferent]
gmap-2025-07-31/src/dynprog_single.h:25:50: note: Function 'Dynprog_single_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2025-07-31/src/dynprog_single.c:430:50: note: Function 'Dynprog_single_gap' argument 13 names different: declaration 'offset2' definition 'goffset'.
gmap-2025-07-31/src/dynprog_single.c:170:35: style: Parameter 'rsequence_nreps' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:171:14: style: Parameter 'gsequence_nreps' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:298:50: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:346:12: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:346:29: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:346:61: style: Parameter 'gsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:346:78: style: Parameter 'gsequence_alt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:685:15: style: Parameter 'rsequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:685:32: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:900:33: style: Parameter 'rsequenceuc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/dynprog_single.c:635:18: warning: Uninitialized variable: gsequence [uninitvar]
gmap-2025-07-31/src/dynprog_single.c:534:20: note: Assuming condition is true
gmap-2025-07-31/src/dynprog_single.c:635:18: note: Uninitialized variable: gsequence
gmap-2025-07-31/src/dynprog_single.c:357:27: style: Variable 'pairdistance_array_type' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/dynprog_single.c:639:14: style: Variable 'finalscore' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/filestring.c:258:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/filestring.c:412:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/exon.c:65:28: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/exon.c:79:22: style: Redundant pointer operation on 'exons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/filestring.c:136:9: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/filestring.c:244:17: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/filestring.c:624:17: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/fopen.c:22:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/fopen.c:12:24: style: Parameter 'read_files_command' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/fopen.c:12:50: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome-write.c:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome-write.c:262:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome-write.c:395:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome-write.c:574:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome-write.c:623:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome-write.c:775:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome-write.c:320:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/genome-write.c:323:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/genome-write.c:703:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/genome-write.c:706:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/genome-write.c:206:45: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome-write.c:218:51: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome-write.c:219:8: style: Variable 'complCode' can be declared as const array [constVariable]
gmap-2025-07-31/src/genome-write.c:234:35: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome-write.c:374:38: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome-write.c:376:50: style: Variable 'segment' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genome-write.c:765:28: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_canonical.c:80:84: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_canonical.c:139:88: style: Parameter 'ref_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_canonical.c:139:111: style: Parameter 'alt_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_canonical.c:219:32: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genome.c:245:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome_sites.c:584:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome_sites.c:229:84: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_sites.c:289:88: style: Parameter 'ref_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_sites.c:289:111: style: Parameter 'alt_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_sites.c:365:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genome_sites.c:532:73: style: Parameter 'old_knownpos' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_sites.c:532:92: style: Parameter 'old_knowni' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome_sites.c:712:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/extension-search.c:2404:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/extension-search.c:2419:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/extension-search.c:296:22: style: Redundant pointer operation on 'set' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/extension-search.c:2014:18: style: Redundant pointer operation on 'univdiagonals_list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/extension-search.c:2014:41: style: Redundant pointer operation on 'auxinfo_list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/extension-search.c:2116:18: style: Redundant pointer operation on 'univdiagonals_list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/extension-search.c:2116:41: style: Redundant pointer operation on 'auxinfo_list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/extension-search.c:2216:18: style: Redundant pointer operation on 'univdiagonals_list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/extension-search.c:2216:41: style: Redundant pointer operation on 'auxinfo_list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/extension-search.c:178:32: style:inconclusive: Function 'Extension_search_setup' argument 1 names different: declaration 'mode' definition 'mode_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/extension-search.h:54:32: note: Function 'Extension_search_setup' argument 1 names different: declaration 'mode' definition 'mode_in'.
gmap-2025-07-31/src/extension-search.c:178:32: note: Function 'Extension_search_setup' argument 1 names different: declaration 'mode' definition 'mode_in'.
gmap-2025-07-31/src/extension-search.c:181:14: style:inconclusive: Function 'Extension_search_setup' argument 8 names different: declaration 'indexdb_fwd_in' definition 'indexdb_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/extension-search.h:57:14: note: Function 'Extension_search_setup' argument 8 names different: declaration 'indexdb_fwd_in' definition 'indexdb_in'.
gmap-2025-07-31/src/extension-search.c:181:14: note: Function 'Extension_search_setup' argument 8 names different: declaration 'indexdb_fwd_in' definition 'indexdb_in'.
gmap-2025-07-31/src/extension-search.c:181:36: style:inconclusive: Function 'Extension_search_setup' argument 9 names different: declaration 'indexdb_rev_in' definition 'indexdb_nonstd_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/extension-search.h:57:40: note: Function 'Extension_search_setup' argument 9 names different: declaration 'indexdb_rev_in' definition 'indexdb_nonstd_in'.
gmap-2025-07-31/src/extension-search.c:181:36: note: Function 'Extension_search_setup' argument 9 names different: declaration 'indexdb_rev_in' definition 'indexdb_nonstd_in'.
gmap-2025-07-31/src/extension-search.c:379:13: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/extension-search.c:520:13: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.c:220:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genomebits.c:159:23: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.c:159:43: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.c:159:59: style: Parameter 'alt_suffix' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits.c:164:7: style: Unused variable: npages0 [unusedVariable]
gmap-2025-07-31/src/genomebits.c:164:16: style: Unused variable: npages1 [unusedVariable]
gmap-2025-07-31/src/genomebits.c:164:25: style: Unused variable: npages2 [unusedVariable]
gmap-2025-07-31/src/genomebits_consec.c:696:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome.c:9015:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9016:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9017:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9018:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9027:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9042:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9043:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9044:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9045:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9054:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9070:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9071:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9072:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9073:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9098:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9099:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9100:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9101:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9110:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9146:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9147:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9148:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9149:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9158:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9169:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9170:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9171:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9172:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9181:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9193:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9194:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9195:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9196:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9217:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9218:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9219:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9220:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9229:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9447:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9448:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9449:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9450:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9468:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9479:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9480:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9481:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9482:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9500:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9512:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9513:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9514:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9515:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9546:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9547:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9548:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9549:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:9567:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genome.c:11080:17: style:inconclusive: Function 'Genome_get_segment_left' argument 5 names different: declaration 'left' definition 'right'. [funcArgNamesDifferent]
gmap-2025-07-31/src/genome.h:132:17: note: Function 'Genome_get_segment_left' argument 5 names different: declaration 'left' definition 'right'.
gmap-2025-07-31/src/genome.c:11080:17: note: Function 'Genome_get_segment_left' argument 5 names different: declaration 'left' definition 'right'.
gmap-2025-07-31/src/genomebits_count.c:912:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genome.c:208:19: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:208:39: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:208:55: style: Parameter 'alt_suffix' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:309:9: style: Variable 'accession' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genome.c:8868:57: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:8985:48: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:9120:57: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:9724:36: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:9767:49: style: Parameter 'blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:11132:23: style: Parameter 'buffer1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:11132:38: style: Parameter 'buffer2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genome.c:10749:25: warning: Uninitialized variable: inbounds_low [uninitvar]
gmap-2025-07-31/src/genome.c:10733:41: note: Assuming condition is false
gmap-2025-07-31/src/genome.c:10749:25: note: Uninitialized variable: inbounds_low
gmap-2025-07-31/src/genome.c:213:7: style: Unused variable: npages [unusedVariable]
gmap-2025-07-31/src/genome.c:8992:17: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9127:17: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9457:9: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genomebits_consec.c:311:38: style:inconclusive: Function 'Genomebits_consecutive_matches_rightward' argument 4 names different: declaration 'left' definition 'querylength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/genomebits_consec.h:19:38: note: Function 'Genomebits_consecutive_matches_rightward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2025-07-31/src/genomebits_consec.c:311:38: note: Function 'Genomebits_consecutive_matches_rightward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2025-07-31/src/genomebits_consec.c:487:37: style:inconclusive: Function 'Genomebits_consecutive_matches_leftward' argument 4 names different: declaration 'left' definition 'querylength'. [funcArgNamesDifferent]
gmap-2025-07-31/src/genomebits_consec.h:23:37: note: Function 'Genomebits_consecutive_matches_leftward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2025-07-31/src/genomebits_consec.c:487:37: note: Function 'Genomebits_consecutive_matches_leftward' argument 4 names different: declaration 'left' definition 'querylength'.
gmap-2025-07-31/src/genomebits_consec.c:56:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_consec.c:317:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/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-2025-07-31/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_consec.c:665:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/src/genome.c:9464:10: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9489:9: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9496:10: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9523:11: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9530:12: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9556:11: style: Variable 'altlow' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genome.c:9563:12: style: Variable 'althigh' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genomebits_kmer.c:445:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genomebits_indel.c:2367:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genomebits_count.c:825:28: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_count.c:839:28: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_count.c:847:28: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_count.c:856:33: style: Redundant pointer operation on 'genomic' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_count.c:867:27: style:inconclusive: Function 'Genomebits_count_setup' argument 1 names different: declaration 'ref' definition 'ref_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/genomebits_count.h:25:27: note: Function 'Genomebits_count_setup' argument 1 names different: declaration 'ref' definition 'ref_in'.
gmap-2025-07-31/src/genomebits_count.c:867:27: note: Function 'Genomebits_count_setup' argument 1 names different: declaration 'ref' definition 'ref_in'.
gmap-2025-07-31/src/genomebits_count.c:867:37: style:inconclusive: Function 'Genomebits_count_setup' argument 2 names different: declaration 'alt' definition 'alt_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/genomebits_count.h:25:34: note: Function 'Genomebits_count_setup' argument 2 names different: declaration 'alt' definition 'alt_in'.
gmap-2025-07-31/src/genomebits_count.c:867:37: note: Function 'Genomebits_count_setup' argument 2 names different: declaration 'alt' definition 'alt_in'.
gmap-2025-07-31/src/genomebits_count.c:60:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_count.c:195:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_count.c:378:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_count.c:606:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:882:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:882:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:882:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:882:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:882:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:882:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:920:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:917:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:917:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:917:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:917:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:917:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:917:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_count.c:917:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/src/genomebits_count.c:56:19: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genomebits_count.c:191:19: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genomebits_kmer.c:40:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/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-2025-07-31/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_kmer.c:414:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/src/genomebits_kmer.c:184:15: style: Variable 'diff_64' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genomebits_kmer.c:199:15: style: Variable 'diff_32' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/genomebits_trim.c:899:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genomebits_mismatches.c:1032:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genomebits_trim.c:65:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:869:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:869:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:869:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:869:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:869:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:869:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:907:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:904:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:904:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:904:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:904:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:904:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:904:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_trim.c:904:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/src/genomicpos.c:57:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/genomicpos.c:34:15: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_mismatches.c:466:39: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:471:43: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:505:39: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:510:43: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:934:40: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:938:44: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:972:40: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:977:44: style: Redundant pointer operation on 'mismatch_positions' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_mismatches.c:67:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_mismatches.c:259:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1002:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1002:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1002:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1002:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1002:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1002:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1040:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1037:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1037:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1037:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1037:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1037:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1037:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_mismatches.c:1037:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/src/getline.c:48:14: style: Variable 'length' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/get-genome.c:149:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:160:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:505:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:605:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:657:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:719:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:795:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:853:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/get-genome.c:982:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/genomebits_indel.c:1631:32: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:1631:49: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:1639:32: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:1639:49: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:1649:38: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:1656:31: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:2288:31: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:2288:48: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:2295:31: style: Redundant pointer operation on 'best_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:2295:48: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:2305:37: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:2312:30: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/genomebits_indel.c:544:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:544:7: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:544:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:544:25: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:776:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:776:7: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:776:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:776:25: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1066:8: style: Local variable 'query_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:45:13: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1066:8: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1067:8: style: Local variable 'genome_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:46:13: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1067:8: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1311:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1311:7: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1311:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1311:25: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1690:8: style: Local variable 'query_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:45:13: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1690:8: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1691:8: style: Local variable 'genome_unk_mismatch_p' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:46:13: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1691:8: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1941:7: style: Local variable 'max_insertionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:41:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1941:7: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:1941:25: style: Local variable 'max_deletionlen' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/genomebits_indel.c:42:12: note: Shadowed declaration
gmap-2025-07-31/src/genomebits_indel.c:1941:25: note: Shadow variable
gmap-2025-07-31/src/genomebits_indel.c:365:54: style: Parameter 'query_high_blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits_indel.c:366:18: style: Parameter 'query_low_blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits_indel.c:366:50: style: Parameter 'query_flags_blocks' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits_indel.c:435:17: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_indel.c:1058:62: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/genomebits_indel.c:1224:44: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits_indel.c:1225:10: style: Parameter 'nmatches_baseline' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits_indel.c:1852:46: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/genomebits_indel.c:1853:12: style: Parameter 'nmatches_baseline' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2337:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:39: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2337:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:413:73: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2337:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:18: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2337:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:414:53: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2337:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:18: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2337:21: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:415:45: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:48: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:460:82: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:20: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:461:55: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:20: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:462:47: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:20: note: Parameter 'snp_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:48: note: Parameter 'snp_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2375:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:463:75: note: Parameter 'snp_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2372:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:46: note: Parameter 'query_high_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2372:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:545:80: note: Parameter 'query_low_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2372:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:25: note: Parameter 'query_flags_shifted' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2372:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:546:60: note: Parameter 'ref_high_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2372:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:25: note: Parameter 'ref_low_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2372:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:547:52: note: Parameter 'ref_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/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-2025-07-31/src/genomebits_indel.c:2372:25: note: You might need to cast the function pointer here
gmap-2025-07-31/src/genomebits.h:549:25: note: Parameter 'mask_flags_ptr' can be declared as pointer to const
gmap-2025-07-31/src/genomebits_indel.c:432:19: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/gmap_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gmap_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gmap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gmap_select.c:43:5: note: Null pointer dereference
gmap-2025-07-31/src/gmap_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gmap_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gmap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gmap_select.c:45:3: note: Null pointer dereference
gmap-2025-07-31/src/gmap_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmap.c:684:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:892:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:4782:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:5058:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:5084:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:5121:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:5166:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:5235:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:5280:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:6068:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:6165:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmap.c:6789:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapl_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:398:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:425:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:467:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:699:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:887:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:1071:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:1315:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapindex.c:1414:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gmapl_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/gmapl_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gmapl_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gmapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gmapl_select.c:43:5: note: Null pointer dereference
gmap-2025-07-31/src/gmapl_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gmapl_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gmapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gmapl_select.c:45:3: note: Null pointer dereference
gmap-2025-07-31/src/gmapl_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/get-genome.c:1895:11: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/get-genome.c:879:25: style: The comparison 'annotationonlyp == 0' is always true. [knownConditionTrueFalse]
gmap-2025-07-31/src/get-genome.c:826:26: note: 'annotationonlyp' is assigned value '0' here.
gmap-2025-07-31/src/get-genome.c:879:25: note: The comparison 'annotationonlyp == 0' is always true.
gmap-2025-07-31/src/get-genome.c:513:40: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:515:32: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:518:24: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:518:39: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:518:55: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:518:71: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:525:40: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:527:32: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:530:24: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:530:39: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:530:55: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:530:71: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:538:40: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:541:38: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:544:30: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:544:45: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:544:61: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:544:77: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/get-genome.c:777:16: style: Local variable 'uniquep' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/get-genome.c:78:13: note: Shadowed declaration
gmap-2025-07-31/src/get-genome.c:777:16: note: Shadow variable
gmap-2025-07-31/src/get-genome.c:245:37: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/get-genome.c:590:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/get-genome.c:639:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/get-genome.c:702:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/get-genome.c:775:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/get-genome.c:948:47: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gsnap_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/gsnap_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gsnap_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gsnap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gsnap_select.c:43:5: note: Null pointer dereference
gmap-2025-07-31/src/gsnap_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gsnap_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gsnap_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gsnap_select.c:45:3: note: Null pointer dereference
gmap-2025-07-31/src/gsnap_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gsnapl_select.c:53:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnapl_select.c:47:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/gsnapl_select.c:43:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gsnapl_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gsnapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gsnapl_select.c:43:5: note: Null pointer dereference
gmap-2025-07-31/src/gsnapl_select.c:45:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_argv [nullPointerOutOfMemory]
gmap-2025-07-31/src/gsnapl_select.c:41:30: note: Assuming allocation function fails
gmap-2025-07-31/src/gsnapl_select.c:41:14: note: Assignment 'new_argv=(char**)malloc((argc+1)*sizeof(char*))', assigned value is 0
gmap-2025-07-31/src/gsnapl_select.c:45:3: note: Null pointer dereference
gmap-2025-07-31/src/gsnapl_select.c:33:9: style: Variable 'dir' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmapindex.c:408:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/gmapindex.c:486:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/gmapindex.c:1405:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/gmapindex.c:1407:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/gmapindex.c:2159:24: style: Comparing expression of type 'unsigned int' against value 4294967295. Condition is always false. [compareValueOutOfTypeRangeError]
gmap-2025-07-31/src/gmapindex.c:2223:24: style: Comparing expression of type 'unsigned int' against value 4294967295. Condition is always false. [compareValueOutOfTypeRangeError]
gmap-2025-07-31/src/gmapindex.c:474:12: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/gmapindex.c:1534:11: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/gmapindex.c:1538:22: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/gmapindex.c:1224:18: style: Redundant pointer operation on 'chrlength_table' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmapindex.c:1254:14: style: Redundant pointer operation on 'accsegmentpos_table' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmapindex.c:1279:14: style: Redundant pointer operation on 'alt_scaffold_info_table' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmapindex.c:455:15: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:682:30: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:682:50: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:863:32: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:863:52: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:1023:26: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:1023:46: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:1304:29: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmapindex.c:1354:25: style: Variable 'source_dbroot' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmapindex.c:923:22: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmapindex.c:1232:12: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmapindex.c:1260:12: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gsnap.c:766:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:969:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:1783:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:2232:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:2296:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:2341:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:2411:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:2453:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:3404:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:3562:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:3588:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:3712:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:4153:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:4366:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:4886:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:302:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:976:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:992:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:1127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:1282:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:1440:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:1567:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:1847:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read-univ.c:1441:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1445:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1479:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1482:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1486:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1492:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1495:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1499:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read-univ.c:1686:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:1686:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:1706:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:1706:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2025:30: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2025:53: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2134:28: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2134:42: style: Redundant pointer operation on 'chrhigh' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2134:54: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2181:42: style: Redundant pointer operation on 'troffset' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2181:55: style: Redundant pointer operation on 'trhigh' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:2181:66: style: Redundant pointer operation on 'trlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read-univ.c:556:33: style: Parameter 'typestring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:654:17: style: Variable 'annotation' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read-univ.c:745:44: style: Parameter 'sam_read_group_id' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:745:69: style: Parameter 'sam_read_group_name' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:746:12: style: Parameter 'sam_read_group_library' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:746:42: style: Parameter 'sam_read_group_platform' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:815:9: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read-univ.c:986:65: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:1091:70: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:1729:45: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:1811:37: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read-univ.c:1813:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read-univ.c:997:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read-univ.c:1009:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read-univ.c:2160:19: style: Variable 'inbounds' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read-univ.c:2206:19: style: Variable 'inbounds' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read.c:127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:1540:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:1560:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:1664:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:1806:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:1888:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable low [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:2303:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:2573:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:2811:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:3085:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:3508:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:4155:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:5220:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:5300:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:5384:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:5473:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:6628:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:6675:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:6719:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:6800:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:6893:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:6993:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:7095:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-read.c:7258:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write-univ.c:458:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write-univ.c:488:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write-univ.c:637:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write-univ.c:274:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/iit-write-univ.c:315:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/iit-write-univ.c:239:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write-univ.c:240:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write-univ.c:252:27: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write-univ.c:253:28: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write-univ.c:74:62: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:101:15: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2025-07-31/src/iit-write-univ.c:113:36: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:113:49: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:113:80: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:130:55: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:130:68: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:131:32: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:160:12: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:379:22: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write-univ.c:380:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write-univ.c:484:21: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write-univ.c:484:34: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write-univ.c:484:42: style: Variable 'annot' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write-univ.c:625:23: style: Parameter 'iitfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write-univ.c:119:10: style: Variable 'iota' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-write.c:576:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write.c:898:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write.c:1225:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable low [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write.c:1479:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write.c:1590:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit-write.c:287:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/iit-write.c:326:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/iit-write.c:676:15: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2025-07-31/src/iit-write.c:670:15: note: First condition
gmap-2025-07-31/src/iit-write.c:676:15: note: Second condition
gmap-2025-07-31/src/iit-write.c:680:15: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2025-07-31/src/iit-write.c:676:15: note: First condition
gmap-2025-07-31/src/iit-write.c:680:15: note: Second condition
gmap-2025-07-31/src/iit-write.c:252:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write.c:253:29: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write.c:265:27: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write.c:266:28: style: Redundant pointer operation on 'index' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write.c:354:21: style: Redundant pointer operation on 'nnodes' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write.c:583:27: style: Redundant pointer operation on 'i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write.c:584:27: style: Redundant pointer operation on 'i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-write.c:84:59: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:111:15: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2025-07-31/src/iit-write.c:123:36: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:123:49: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:123:76: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:140:55: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:140:68: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:141:28: style: Parameter 'intervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:170:12: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:427:23: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:428:23: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:441:58: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:485:22: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:486:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:492:58: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:626:14: style: Parameter 'nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:626:31: style: Parameter 'nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:626:44: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:626:65: style: Parameter 'cum_nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:633:9: style: Variable 'divstring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:717:15: style: Parameter 'nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:717:32: style: Parameter 'nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:717:45: style: Parameter 'cum_nintervals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:717:66: style: Parameter 'cum_nnodes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:722:9: style: Variable 'divstring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:794:48: style: Parameter 'alphas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:794:61: style: Parameter 'betas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:794:73: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:794:86: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:844:57: style: Parameter 'alphas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:844:70: style: Parameter 'betas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:844:82: style: Parameter 'sigmas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:844:95: style: Parameter 'omegas' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:894:21: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:894:34: style: Variable 'fieldstring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:894:48: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:894:56: style: Variable 'annot' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:1208:21: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:1208:34: style: Variable 'fieldstring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:1208:48: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-write.c:1466:18: style: Parameter 'iitfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-write.c:129:10: style: Variable 'iota' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-write.c:631:17: style: Variable 'pointer' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit_dump.c:47:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_dump.c:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_dump.c:171:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_dump.c:226:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_dump.c:102:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_get.c:90:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:101:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:287:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:352:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:459:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:716:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:815:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:882:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:997:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_get.c:286:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_get.c:351:16: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_get.c:373:16: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_get.c:458:16: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_get.c:1176:18: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/iit_get.c:1107:5: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/iit_get.c:1336:7: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/iit_get.c:1186:20: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/iit_get.c:645:16: style: Variable 'annotation' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/iit_get.c:640:16: note: annotation is assigned
gmap-2025-07-31/src/iit_get.c:645:16: note: annotation is overwritten
gmap-2025-07-31/src/iit_get.c:469:27: style: Redundant pointer operation on 'total' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:552:35: style: Redundant pointer operation on 'lastcoord' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:555:30: style: Redundant pointer operation on 'lastcoord' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:706:77: style: Redundant pointer operation on 'divstring' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:706:91: style: Redundant pointer operation on 'coordstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:706:106: style: Redundant pointer operation on 'coordend' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:730:24: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:754:35: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:756:20: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:759:19: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:759:34: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:759:50: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:759:66: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:781:35: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:783:26: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:787:25: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:787:40: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:787:56: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:787:72: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:806:77: style: Redundant pointer operation on 'divstring' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:806:91: style: Redundant pointer operation on 'coordstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:806:106: style: Redundant pointer operation on 'coordend' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:822:29: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:838:30: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:859:30: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:875:77: style: Redundant pointer operation on 'divstring' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:875:91: style: Redundant pointer operation on 'coordstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:875:106: style: Redundant pointer operation on 'coordend' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:895:36: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:897:37: style: Redundant pointer operation on 'leftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:897:52: style: Redundant pointer operation on 'nleftflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:897:68: style: Redundant pointer operation on 'rightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:897:84: style: Redundant pointer operation on 'nrightflanks' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_get.c:169:22: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_get.c:179:25: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_get.c:199:32: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_get.c:284:9: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_get.c:313:19: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_get.c:325:50: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_get.c:395:54: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_get.c:657:17: style: Variable 'annotation' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_get.c:775:16: style: Variable 'nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit_get.c:843:25: style: Variable 'typeint' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit_get.c:1112:26: style: Variable 'universalp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit_store.c:88:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:99:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:296:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:458:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:522:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:604:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:777:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:860:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:965:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/iit_store.c:242:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_store.c:243:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:244:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:249:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_store.c:250:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:251:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:266:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_store.c:268:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:269:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:322:15: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/iit_store.c:330:9: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:346:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:491:13: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/iit_store.c:748:32: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:749:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:768:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:776:16: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/iit_store.c:785:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/iit_store.c:793:13: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/iit_store.c:688:7: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/iit_store.c:295:7: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/iit_store.c:304:29: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/iit_store.c:379:29: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/iit_store.c:453:14: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
gmap-2025-07-31/src/iit_store.c:562:5: warning: If memory allocation fails, then there is a possible null pointer dereference: header [nullPointerOutOfMemory]
gmap-2025-07-31/src/iit_store.c:561:29: note: Assuming allocation function fails
gmap-2025-07-31/src/iit_store.c:561:14: note: Assignment 'header=(char*)malloc((line_length+2)*sizeof(char))', assigned value is 0
gmap-2025-07-31/src/iit_store.c:562:5: note: Null pointer dereference
gmap-2025-07-31/src/iit_store.c:245:25: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:245:61: style: Redundant pointer operation on 'end' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:252:20: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:270:25: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:270:61: style: Redundant pointer operation on 'end' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:357:24: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:360:22: style: Redundant pointer operation on 'start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:360:32: style: Redundant pointer operation on 'end' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:568:35: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:568:58: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:575:53: style: Redundant pointer operation on 'divlist' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:575:65: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:576:25: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:640:32: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:641:5: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:647:50: style: Redundant pointer operation on 'divlist' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:647:62: style: Redundant pointer operation on 'typelist' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:648:9: style: Redundant pointer operation on 'valuep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit_store.c:217:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_store.c:234:54: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_store.c:287:77: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_store.c:518:9: style: Variable 'line' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_store.c:765:39: style: Parameter 'labelstr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit_store.c:809:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_store.c:825:29: style: Variable 'chr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_store.c:825:35: style: Variable 'idptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit_store.c:938:9: style: Variable 'inputfile' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gsnap.c:2242:7: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
gmap-2025-07-31/src/gsnap.c:4651:5: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/gsnap.c:4848:5: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/gsnap.c:4851:5: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/gsnap.c:4937:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/gsnap.c:5167:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/gsnap.c:5278:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/inbuffer.c:263:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/gsnap.c:1815:5: style: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/gsnap.c:1331:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1331:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1331:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1364:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1364:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1364:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1384:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1384:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1384:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1417:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1417:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1417:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1455:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1455:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1455:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1564:39: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1564:58: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:1564:79: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:2231:21: style: Redundant pointer operation on 'part_modulus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:2242:21: style: Redundant pointer operation on 'part_interval' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:3420:40: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:3468:37: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:3528:43: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:3600:37: style: Redundant pointer operation on 'any_circular_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:3390:8: style: Local variable 'fastq_format_p' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/gsnap.c:290:13: note: Shadowed declaration
gmap-2025-07-31/src/gsnap.c:3390:8: note: Shadow variable
gmap-2025-07-31/src/gsnap.c:3553:14: style: Local variable 'transcript_iit' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/gsnap.c:228:19: note: Shadowed declaration
gmap-2025-07-31/src/gsnap.c:3553:14: note: Shadow variable
gmap-2025-07-31/src/gsnap.c:3578:14: style: Local variable 'chromosome_iit' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/gsnap.c:237:19: note: Shadowed declaration
gmap-2025-07-31/src/gsnap.c:3578:14: note: Shadow variable
gmap-2025-07-31/src/iit-read.c:7128:34: style: Condition 'pos<=exonend' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/iit-read.c:7116:17: note: Assuming that condition 'pos>exonend' is not redundant
gmap-2025-07-31/src/iit-read.c:7128:34: note: Condition 'pos<=exonend' is always true
gmap-2025-07-31/src/iit-read.c:7181:34: style: Condition 'pos>=exonend' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/iit-read.c:7169:17: note: Assuming that condition 'pos<exonend' is not redundant
gmap-2025-07-31/src/iit-read.c:7181:34: note: Condition 'pos>=exonend' is always true
gmap-2025-07-31/src/iit-read.c:7291:34: style: Condition 'pos<=exonend' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/iit-read.c:7279:17: note: Assuming that condition 'pos>exonend' is not redundant
gmap-2025-07-31/src/iit-read.c:7291:34: note: Condition 'pos<=exonend' is always true
gmap-2025-07-31/src/iit-read.c:7344:34: style: Condition 'pos>=exonend' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/iit-read.c:7332:17: note: Assuming that condition 'pos<exonend' is not redundant
gmap-2025-07-31/src/iit-read.c:7344:34: note: Condition 'pos>=exonend' is always true
gmap-2025-07-31/src/iit-read.c:2579:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2591:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2595:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2603:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2607:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2612:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2616:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2624:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2632:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2639:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2643:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2653:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2656:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2660:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2670:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2673:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2677:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2684:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2690:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2693:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:2697:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3091:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3106:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3110:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3130:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3134:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3139:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3143:2: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3168:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3172:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3178:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3181:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3190:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3193:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3197:5: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3207:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3210:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3214:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3232:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3235:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3239:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3258:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3261:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3265:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3311:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3314:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/iit-read.c:3318:7: error: Resource leak: fp [resourceLeak]
gmap-2025-07-31/src/gsnap.c:2229:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gsnap.c:2289:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gsnap.c:2330:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gsnap.c:2393:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gsnap.c:3552:15: style: Parameter 'transcriptomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gsnap.c:3552:42: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gsnap.c:3577:55: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gsnap.c:3577:75: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gsnap.c:4315:22: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmap.c:5043:14: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/gmap.c:5049:21: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/gsnap.c:1835:15: style: Modulo of one is always equal to zero [moduloofone]
gmap-2025-07-31/src/iit-read.c:1982:19: portability: Casting between char * and double * which have an incompatible binary data representation. [invalidPointerCast]
gmap-2025-07-31/src/iit-read.c:3772:15: style: The comparison 'divread == READ_ALL' is always true because 'divread' and 'READ_ALL' represent the same value. [knownConditionTrueFalse]
gmap-2025-07-31/src/iit-read.c:3479:23: note: 'divread' is assigned value 'READ_ALL' here.
gmap-2025-07-31/src/iit-read.c:3772:15: note: The comparison 'divread == READ_ALL' is always true because 'divread' and 'READ_ALL' represent the same value.
gmap-2025-07-31/src/gmap.c:5094:7: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
gmap-2025-07-31/src/gmap.c:6673:3: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/gmap.c:6847:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/gmap.c:6923:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/gmap.c:7118:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/iit-read.c:3909:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read.c:3909:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read.c:3928:21: style: Redundant pointer operation on 'min' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read.c:3928:29: style: Redundant pointer operation on 'max' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/iit-read.c:5960:30: style:inconclusive: Function 'IIT_get_exact_multiple' argument 1 names different: declaration 'nmatches' definition 'nexactmatches'. [funcArgNamesDifferent]
gmap-2025-07-31/src/iit-read.h:209:30: note: Function 'IIT_get_exact_multiple' argument 1 names different: declaration 'nmatches' definition 'nexactmatches'.
gmap-2025-07-31/src/iit-read.c:5960:30: note: Function 'IIT_get_exact_multiple' argument 1 names different: declaration 'nmatches' definition 'nexactmatches'.
gmap-2025-07-31/src/iit-read.c:106:23: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:340:27: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:405:28: style: Parameter 'typestring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:429:29: style: Parameter 'fieldstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:658:39: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:775:9: style: Variable 'label' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:812:9: style: Variable 'labelptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:812:20: style: Variable 'annotptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:814:17: style: Variable 'annotation' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:1249:40: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:1550:61: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:1650:60: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:1790:87: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:1862:65: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:2541:40: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:2788:31: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:3039:33: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:3950:40: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:4104:32: style: Parameter 'label' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:4106:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:5458:75: style: Parameter 'types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:5833:9: style: Parameter 'types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:6493:9: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:6511:33: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:6581:49: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:6604:13: style: Parameter 'genes_chrnum_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:6606:24: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:6651:14: style: Parameter 'genes_chrnum_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:6653:24: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:6700:24: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:6770:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:6888:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:6977:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:7211:64: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/iit-read.c:7537:62: style: Parameter 'matches' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/gmap.c:4796:5: style: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/gmap.c:1463:34: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1463:53: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1463:71: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1463:87: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1609:34: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1609:53: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1609:71: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1609:87: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:1795:18: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2057:32: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2057:46: style: Redundant pointer operation on 'chrhigh' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2057:58: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2077:32: style: Redundant pointer operation on 'chroffset' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2077:46: style: Redundant pointer operation on 'chrhigh' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2077:58: style: Redundant pointer operation on 'chrlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2626:46: style: Redundant pointer operation on 'chimeraequivpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2627:11: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2627:22: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2627:33: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2627:47: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2654:12: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2654:23: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2654:34: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2654:48: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2655:18: style: Redundant pointer operation on 'donor_watsonp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2655:36: style: Redundant pointer operation on 'acceptor_watsonp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2655:57: style: Redundant pointer operation on 'donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:2655:72: style: Redundant pointer operation on 'acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:4212:31: style: Redundant pointer operation on 'mergedp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:4319:33: style: Redundant pointer operation on 'mergedp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:4319:45: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:4453:43: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:4471:20: style: Redundant pointer operation on 'chimera' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:4647:37: style: Redundant pointer operation on 'fp_failedinput' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:5083:21: style: Redundant pointer operation on 'part_modulus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gmap.c:5094:21: style: Redundant pointer operation on 'part_interval' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/gsnap.c:892:18: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gsnap.c:892:30: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gsnap.c:892:16: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gsnap.c:892:28: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gsnap.c:1703:26: style: Variable 'max_localdb_nregions' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gsnap.c:1704:24: style: Variable 'max_nintersections' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap.c:6051:14: style: Local variable 'inbuffer' shadows outer variable [shadowVariable]
gmap-2025-07-31/src/gmap.c:504:19: note: Shadowed declaration
gmap-2025-07-31/src/gmap.c:6051:14: note: Shadow variable
gmap-2025-07-31/src/gsnap.c:4328:12: style: Unused variable: worker_id [unusedVariable]
gmap-2025-07-31/src/gmap.c:5037:9: style: Variable 'typestring' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmap.c:5037:31: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmap.c:5081:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmap.c:5114:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmap.c:5155:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/gmap.c:5217:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/iit-read.c:1704:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read.c:1725:21: style: Variable 'items_read' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read.c:2666:13: style: Variable 'nfields' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read.c:2731:12: style: Variable 'offset' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/iit-read.c:2747:12: style: Variable 'offset' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap.c:817:18: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap.c:817:30: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap.c:817:16: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap.c:817:28: style: Variable 'y' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap.c:1510:22: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/gmap.c:6117:16: style: Variable 'nextchar' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/indexdb-cat.c:92:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb-cat.c:146:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb-cat.c:650:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb-cat.c:928:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indel.c:353:45: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/indel.c:357:45: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/indel.c:646:45: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/indel.c:650:45: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/indexdb-write.c:531:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb-write.c:1233:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb-write.c:1995:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb-write.c:2510:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb-cat.c:821:25: style: Comparing expression of type 'unsigned int' against value 4294967295. Condition is always true. [compareValueOutOfTypeRangeError]
gmap-2025-07-31/src/indexdb-cat.c:822:5: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/indexdb-cat.c:826:5: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/indexdb-cat.c:900:3: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/indexdb-cat.c:900:3: warning: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'unsigned int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/indexdb-cat.c:126:15: style: Parameter 'new_positions_filename' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb-cat.c:127:43: style: Parameter 'genome_univcoord' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb-cat.c:183:10: style: Variable 'indexdb' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/indexdb-cat.c:735:21: style: Variable 'ifilenames' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/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-2025-07-31/src/intersect-approx-indices-uint4.c:210:31: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-approx-indices-uint4.c:246:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/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-2025-07-31/src/intersect-approx-indices-uint4.c:210:31: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-approx-indices-uint4.c:250:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/indexdb.c:477:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:755:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:1253:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:1565:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:1704:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:1761:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:1842:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:2050:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/indexdb.c:2805:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mask [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/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-2025-07-31/src/intersect-approx-indices-uint8.c:205:30: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-approx-indices-uint8.c:237:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/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-2025-07-31/src/intersect-approx-indices-uint8.c:205:30: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-approx-indices-uint8.c:241:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/indexdb-write.c:786:3: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/indexdb-write.c:467:30: style: Parameter 'destdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb-write.c:473:58: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb-write.c:474:9: style: Variable 'uppercaseCode' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb-write.c:476:9: style: Variable 'filesuffix' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb-write.c:1920:54: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb-write.c:1922:9: style: Variable 'uppercaseCode' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb-write.c:2468:7: style: Unused variable: offsetsmeta_fd [unusedVariable]
gmap-2025-07-31/src/indexdb-write.c:2468:23: style: Unused variable: offsetsstrm_fd [unusedVariable]
gmap-2025-07-31/src/indexdb-write.c:2481:32: style: Unused variable: offsetsstrm_access [unusedVariable]
gmap-2025-07-31/src/intersect-concordance-uint4.c:269:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2025-07-31/src/intersect-concordance-uint4.c:236:31: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-concordance-uint4.c:269:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/intersect-concordance-uint4.c:273:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2025-07-31/src/intersect-concordance-uint4.c:236:31: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-concordance-uint4.c:273:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/intersect-higher-large.c:146:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-higher-large.c:192:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-higher-large.c:234:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-higher-large.c:270:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-higher-large.c:158:20: style: Condition '1||B_value+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-higher-large.c:202:20: style: Condition '1||A_value+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-higher-large.c:243:18: style: Condition '1||B_value+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-higher-large.c:278:18: style: Condition '1||A_value+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-higher-large.c:132:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-higher-large.c:179:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-higher-large.c:223:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-higher-large.c:259:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-concordance-uint8.c:261:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2025-07-31/src/intersect-concordance-uint8.c:229:30: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-concordance-uint8.c:261:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/intersect-concordance-uint8.c:265:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2025-07-31/src/intersect-concordance-uint8.c:229:30: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-concordance-uint8.c:265:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/intersect-higher-small.c:198:8: style: Condition '1||(*A)+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-higher-small.c:204:8: style: Condition '1||(*B)+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-higher-small.c:243:13: style: Condition '1||(*A)+diagtermA>=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-higher-small.c:249:13: style: Condition '1||(*B)+diagtermB>=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-indices2-large.c:289:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-indices2-large.c:331:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-indices-small.c:131:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-indices-uint8.c:123:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-large.c:160:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-large.c:1716:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-large.c:91:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-indices2-large.c:125:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-indices2-large.c:210:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-indices2-large.c:284:16: style: Variable 'initB' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-indices2-large.c:325:16: style: Variable 'initA' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-lower-large.c:146:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-lower-large.c:192:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-lower-large.c:234:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-lower-large.c:270:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-indices2-small.c:130:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/intersect-lower-large.c:158:20: style: Condition '1||B_value+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-lower-large.c:202:20: style: Condition '1||A_value+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-lower-large.c:243:18: style: Condition '1||B_value+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-lower-large.c:278:18: style: Condition '1||A_value+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-lower-large.c:132:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-lower-large.c:179:48: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-lower-large.c:223:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-lower-large.c:259:56: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-lower-small.c:198:8: style: Condition '1||(*A)+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-lower-small.c:204:8: style: Condition '1||(*B)+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-lower-small.c:245:13: style: Condition '1||(*A)+diagtermA<=(*B)+diagtermB' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-lower-small.c:252:13: style: Condition '1||(*B)+diagtermB<=(*A)+diagtermA' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/intersect-uint2.c:73:20: style: Parameter 'set1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intersect-small.c:1120:44: warning: Uninitialized variable: diagonals [uninitvar]
gmap-2025-07-31/src/intersect-small.c:1116:18: note: Assuming condition is true
gmap-2025-07-31/src/intersect-small.c:1120:44: note: Uninitialized variable: diagonals
gmap-2025-07-31/src/intersect-small.c:1128:44: error: Uninitialized variable: diagonals [legacyUninitvar]
gmap-2025-07-31/src/intersect-small.c:1140:28: error: Uninitialized variable: diagonals [legacyUninitvar]
gmap-2025-07-31/src/intersect-small.c:1148:28: error: Uninitialized variable: diagonals [legacyUninitvar]
gmap-2025-07-31/src/intersect-small.c:85:11: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/interval.c:231:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/interval.c:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/intersect-wdups-indices.c:228:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2025-07-31/src/intersect-wdups-indices.c:193:31: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-wdups-indices.c:228:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/intersect-wdups-indices.c:232:33: style: Same expression on both sides of '-' because 'A' and 'initA' represent the same value. [duplicateExpression]
gmap-2025-07-31/src/intersect-wdups-indices.c:193:31: note: 'initA' is assigned value 'A' here.
gmap-2025-07-31/src/intersect-wdups-indices.c:232:33: note: Same expression on both sides of '-' because 'A' and 'initA' represent the same value.
gmap-2025-07-31/src/intlist.c:406:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2025-07-31/src/intlist.c:401:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2025-07-31/src/intlist.c:403:20: note: Assuming condition is false
gmap-2025-07-31/src/intlist.c:406:10: note: Null pointer dereference
gmap-2025-07-31/src/intlist.c:427:3: warning: Possible null pointer dereference: last [nullPointer]
gmap-2025-07-31/src/intlist.c:421:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2025-07-31/src/intlist.c:423:20: note: Assuming condition is false
gmap-2025-07-31/src/intlist.c:427:3: note: Null pointer dereference
gmap-2025-07-31/src/intlist.c:449:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2025-07-31/src/intlist.c:444:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2025-07-31/src/intlist.c:446:26: note: Assuming condition is false
gmap-2025-07-31/src/intlist.c:449:10: note: Null pointer dereference
gmap-2025-07-31/src/intlist.c:362:26: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intlist.c:522:18: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/intlist.c:523:18: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/intlist.c:536:18: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/intlist.c:537:18: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/intlist.c:554:18: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/intlist.c:555:18: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/intlist.c:761:31: style: Parameter 'deletep' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/intlist.c:377:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2025-07-31/src/intlistpool.c:221:29: style:inconclusive: Function 'Intlistpool_push' argument 1 names different: declaration 'intlist' definition 'list'. [funcArgNamesDifferent]
gmap-2025-07-31/src/intlistpool.h:71:29: note: Function 'Intlistpool_push' argument 1 names different: declaration 'intlist' definition 'list'.
gmap-2025-07-31/src/intlistpool.c:221:29: note: Function 'Intlistpool_push' argument 1 names different: declaration 'intlist' definition 'list'.
gmap-2025-07-31/src/junction.c:375:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/junction.c:81:13: style: Condition '0&&this->splice_distance==0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/junction.c:106:28: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/junction.c:121:22: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/indexdb.c:2460:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/indexdb.c:2500:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/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-2025-07-31/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-2025-07-31/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-2025-07-31/src/indexdb.c:541:4: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/indexdb.c:938:4: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/indexdb.c:436:37: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:436:53: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:436:75: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:443:55: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb.c:452:18: style: Variable 'entry' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb.c:708:36: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:708:52: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:708:74: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:728:45: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb.c:735:18: style: Variable 'entry' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb.c:1243:59: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:1243:81: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:1552:61: style: Parameter 'idx_filesuffix' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:1553:9: style: Parameter 'snps_root' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/indexdb.c:2771:9: style: Variable 'uppercaseCode' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb.c:2776:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/indexdb.c:379:18: style: Variable 'oligospace' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/knownindels.c:121:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/knownindels.c:219:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/knownindels.c:278:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/knownindels.c:318:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/list.c:442:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2025-07-31/src/list.c:437:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2025-07-31/src/list.c:439:20: note: Assuming condition is false
gmap-2025-07-31/src/list.c:442:10: note: Null pointer dereference
gmap-2025-07-31/src/list.c:190:18: style:inconclusive: Function 'List_head_set' argument 1 names different: declaration 'list' definition 'this'. [funcArgNamesDifferent]
gmap-2025-07-31/src/list.h:223:30: note: Function 'List_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2025-07-31/src/list.c:190:18: note: Function 'List_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2025-07-31/src/list.c:521:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/list.c:360:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2025-07-31/src/knownsplicing.c:197:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/knownsplicing.c:464:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/knownsplicing.c:490:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/knownsplicing.c:990:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/knownindels.c:169:22: style: Parameter 'raw_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownindels.c:169:58: style: Parameter 'raw_counts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownindels.c:253:22: warning: Uninitialized variable: allocp [uninitvar]
gmap-2025-07-31/src/knownindels.c:230:17: note: Assuming condition is false
gmap-2025-07-31/src/knownindels.c:253:22: note: Uninitialized variable: allocp
gmap-2025-07-31/src/localdb-write.c:504:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/kmer-search.c:291:49: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:294:50: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:639:35: style: Redundant pointer operation on '_univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:639:54: style: Redundant pointer operation on 'auxinfo' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:639:66: style: Redundant pointer operation on 'pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:776:35: style: Redundant pointer operation on '_univdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:776:54: style: Redundant pointer operation on 'auxinfo' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:776:66: style: Redundant pointer operation on 'pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:853:25: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:853:50: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:853:68: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:864:26: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:864:52: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:864:71: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/kmer-search.c:194:28: style:inconclusive: Function 'Kmer_exact1' argument 10 names different: declaration 'querystart' definition 'kmer_querystart'. [funcArgNamesDifferent]
gmap-2025-07-31/src/kmer-search.h:47:28: note: Function 'Kmer_exact1' argument 10 names different: declaration 'querystart' definition 'kmer_querystart'.
gmap-2025-07-31/src/kmer-search.c:194:28: note: Function 'Kmer_exact1' argument 10 names different: declaration 'querystart' definition 'kmer_querystart'.
gmap-2025-07-31/src/kmer-search.c:194:49: style:inconclusive: Function 'Kmer_exact1' argument 11 names different: declaration 'queryend' definition 'kmer_queryend'. [funcArgNamesDifferent]
gmap-2025-07-31/src/kmer-search.h:47:44: note: Function 'Kmer_exact1' argument 11 names different: declaration 'queryend' definition 'kmer_queryend'.
gmap-2025-07-31/src/kmer-search.c:194:49: note: Function 'Kmer_exact1' argument 11 names different: declaration 'queryend' definition 'kmer_queryend'.
gmap-2025-07-31/src/kmer-search.c:386:18: style: Parameter 'exhaustive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/kmer-search.c:386:35: style: Parameter 'qstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/kmer-search.c:386:49: style: Parameter 'qends' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/kmer-search.c:456:16: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:393:8: style: Variable 'kmer' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/localdb-write.c:364:8: note: kmer is assigned
gmap-2025-07-31/src/localdb-write.c:393:8: note: kmer is overwritten
gmap-2025-07-31/src/localdb-write.c:115:64: style: Parameter 'sarray16' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:116:11: style: Parameter 'gbuffer16' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:120:9: style: Variable 'oligo' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/localdb-write.c:168:62: style: Parameter 'saindex16' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:224:65: style: Parameter 'intstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:482:22: style: Parameter 'saindex16file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:482:43: style: Parameter 'sarray16file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:483:15: style: Parameter 'sarray8file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-write.c:483:34: style: Parameter 'sasort16file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/mapq.c:76:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mapq.c:164:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/match.c:174:32: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/match.c:175:9: style: Variable 'genomicseg_ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/mapq.c:65:31: style: Parameter 'quality_string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/mapq.c:154:27: style: Parameter 'genomic_diff' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/mapq.c:154:47: style: Parameter 'quality_string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownsplicing.c:490:84: warning: Either the condition '(line=Getline(fp))==NULL' is redundant or there is possible null pointer dereference: line. [nullPointerRedundantCheck]
gmap-2025-07-31/src/knownsplicing.c:489:28: note: Assuming that condition '(line=Getline(fp))==NULL' is not redundant
gmap-2025-07-31/src/knownsplicing.c:490:84: note: Null pointer dereference
gmap-2025-07-31/src/knownsplicing.c:522:81: warning: Either the condition '(line=Getline(fp))!=NULL' is redundant or there is possible null pointer dereference: line. [nullPointerRedundantCheck]
gmap-2025-07-31/src/knownsplicing.c:495:31: note: Assuming that condition '(line=Getline(fp))!=NULL' is not redundant
gmap-2025-07-31/src/knownsplicing.c:522:81: note: Null pointer dereference
gmap-2025-07-31/src/knownsplicing.c:554:82: warning: Either the condition '(line=Getline(fp))!=NULL' is redundant or there is possible null pointer dereference: line. [nullPointerRedundantCheck]
gmap-2025-07-31/src/knownsplicing.c:527:31: note: Assuming that condition '(line=Getline(fp))!=NULL' is not redundant
gmap-2025-07-31/src/knownsplicing.c:554:82: note: Null pointer dereference
gmap-2025-07-31/src/knownsplicing.c:586:85: warning: Either the condition '(line=Getline(fp))!=NULL' is redundant or there is possible null pointer dereference: line. [nullPointerRedundantCheck]
gmap-2025-07-31/src/knownsplicing.c:559:31: note: Assuming that condition '(line=Getline(fp))!=NULL' is not redundant
gmap-2025-07-31/src/knownsplicing.c:586:85: note: Null pointer dereference
gmap-2025-07-31/src/knownsplicing.c:646:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:646:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:673:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:673:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:700:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:700:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:727:20: style: Redundant pointer operation on 'low_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:727:33: style: Redundant pointer operation on 'high_rank' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/knownsplicing.c:962:59: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownsplicing.c:1056:33: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownsplicing.c:1056:55: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownsplicing.c:1076:34: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownsplicing.c:1076:56: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/knownsplicing.c:106:18: style: Variable 'nintervals' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/knownsplicing.c:187:21: style: Variable 'pvalue' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/md5.c:207:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/md5.c:220:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/md5.c:77:39: style: Parameter 'input' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/md5.c:92:39: style: Parameter 'input' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:2594:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:527:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:623:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:697:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:782:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:847:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:911:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:953:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:1045:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:1126:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:1199:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:1274:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:1735:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/mem.c:952:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/mem.c:1044:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/mem.c:1125:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/mem.c:1198:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/mem.c:1273:13: style: Checking if unsigned expression 'count' is less than zero. [unsignedLessThanZero]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:172:23: style:inconclusive: Function 'Merge_diagonals' argument 1 names different: declaration 'nelts1' definition 'nelts'. [funcArgNamesDifferent]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.h:14:23: note: Function 'Merge_diagonals' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:172:23: note: Function 'Merge_diagonals' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:296:29: style:inconclusive: Function 'Merge_diagonals_uint4' argument 1 names different: declaration 'nelts1' definition 'nelts'. [funcArgNamesDifferent]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.h:20:29: note: Function 'Merge_diagonals_uint4' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:296:29: note: Function 'Merge_diagonals_uint4' argument 1 names different: declaration 'nelts1' definition 'nelts'.
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:120:35: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:121:13: style: Parameter 'diagterm_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:122:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:176:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:248:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:249:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint4.c:300:10: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:121:13: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:121:36: style: Parameter 'diagterm_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:122:18: style: Variable 'stream_high' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:123:10: style: Variable 'stream_low' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:179:18: style: Variable 'stream_high' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:180:10: style: Variable 'stream_low' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:252:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:253:16: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:304:16: style: Variable 'stream' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:148:17: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
gmap-2025-07-31/src/merge-diagonals-heap-uint8.c:201:15: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
gmap-2025-07-31/src/merge-diagonals-simd-uint4.c:126:13: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-simd-uint4.c:126:36: style: Parameter 'diagterm_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-simd-uint4.c:354:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-simd-uint4.c:421:11: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/merge-diagonals-simd-uint8.c:336:10: style: Parameter 'streamsize_array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/merge-diagonals-simd-uint8.c:403:9: style: Variable 'out' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/merge-uint4.c:269:26: style: Variable 'Aend' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-uint4.c:269:33: style: Variable 'Bend' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-uint4.c:270:16: style: Unused variable: nextA [unusedVariable]
gmap-2025-07-31/src/merge-uint4.c:270:23: style: Unused variable: nextB [unusedVariable]
gmap-2025-07-31/src/merge-uint8.c:243:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/merge-uint8.c:226:19: style: Variable 'Aend' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-uint8.c:226:26: style: Variable 'Bend' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/merge-uint8.c:227:9: style: Unused variable: nextA [unusedVariable]
gmap-2025-07-31/src/merge-uint8.c:227:16: style: Unused variable: nextB [unusedVariable]
gmap-2025-07-31/src/method.c:12:20: style: Parameter 'methodp' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/nr-x.c:14:17: style: Variable 'cof' can be declared as const array [constVariable]
gmap-2025-07-31/src/oligo.c:504:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/oligo.c:224:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:224:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:224:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:226:38: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:226:51: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:226:63: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:232:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:232:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:232:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:356:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:356:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:356:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:358:38: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:358:51: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:358:63: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:364:25: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:364:38: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:364:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:378:35: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:378:48: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:378:60: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:381:33: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:381:46: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:381:58: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:399:35: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:399:48: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:399:60: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:402:33: style: Redundant pointer operation on 'querypos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:402:46: style: Redundant pointer operation on 'forward' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/oligo.c:402:58: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/maxent.c:98998:16: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99020:37: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99039:24: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99062:21: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99097:42: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99128:29: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99246:54: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99337:57: style: Parameter 'nucleotides' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/maxent.c:99352:22: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:1842:16: style: Condition 'nptrs5>0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/localdb-read.c:1819:19: note: Assuming that condition 'highi5>=lowi5' is not redundant
gmap-2025-07-31/src/localdb-read.c:1822:29: note: Assignment 'nptrs5=highi5-lowi5+1', assigned value is less than 1
gmap-2025-07-31/src/localdb-read.c:1842:16: note: Condition 'nptrs5>0' is always false
gmap-2025-07-31/src/localdb-read.c:2284:42: style: Condition '(matchlength=trimpos3-trimpos5)<=0' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/localdb-read.c:2246:17: note: Assuming that condition 'trimpos3<=pos5' is not redundant
gmap-2025-07-31/src/localdb-read.c:2247:17: note: Assignment 'trimpos5=pos5', assigned value is symbolic=trimpos3
gmap-2025-07-31/src/localdb-read.c:2284:42: note: Condition '(matchlength=trimpos3-trimpos5)<=0' is always true
gmap-2025-07-31/src/localdb-read.c:964:25: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:1004:27: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:1717:24: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:1717:40: style: Redundant pointer operation on 'univdiags' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2427:37: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2427:53: style: Redundant pointer operation on 'univdiags_alloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2442:28: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2442:44: style: Redundant pointer operation on 'univdiags_alloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2458:28: style: Redundant pointer operation on 'trimmedp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2458:41: style: Redundant pointer operation on 'matchlength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2458:57: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:2458:73: style: Redundant pointer operation on 'univdiags_alloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/localdb-read.c:192:78: style: Parameter 'SA' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:193:14: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:324:17: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:344:22: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:376:79: style: Parameter 'saindex' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:376:98: style: Parameter 'SA' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:1906:28: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/localdb-read.c:1956:34: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/localdb-read.c:2022:72: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/localdb-read.c:2024:13: style: Variable 'saindex16' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/localdb-read.c:2025:13: style: Variable 'sasort16' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/localdb-read.c:2568:20: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:2568:40: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/localdb-read.c:198:16: style: Variable 'nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/localdb-read.c:382:16: style: Variable 'nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/orderstat.c:203:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/orderstat.c:217:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/orderstat.c:231:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/orderstat.c:245:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/orderstat.c:198:29: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/orderstat.c:212:23: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/orderstat.c:226:33: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/orderstat.c:240:33: style: Parameter 'vector' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/outbuffer.c:194:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/outbuffer.c:1198:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/outbuffer.c:1342:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/outbuffer.c:1361:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/outbuffer.c:1342:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/outbuffer.c:1487:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/outbuffer.c:1503:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/outbuffer.c:1487:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/outbuffer.c:1168:60: style:inconclusive: Function 'Outbuffer_print_filestrings' argument 2 names different: declaration 'fp_failedinput_1' definition 'fp_failedinput'. [funcArgNamesDifferent]
gmap-2025-07-31/src/outbuffer.h:70:60: note: Function 'Outbuffer_print_filestrings' argument 2 names different: declaration 'fp_failedinput_1' definition 'fp_failedinput'.
gmap-2025-07-31/src/outbuffer.c:1168:60: note: Function 'Outbuffer_print_filestrings' argument 2 names different: declaration 'fp_failedinput_1' definition 'fp_failedinput'.
gmap-2025-07-31/src/outbuffer.c:149:25: style: Parameter 'failedinput_root' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/output.c:913:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/output.c:85:57: style:inconclusive: Function 'Output_setup' argument 14 names different: declaration 'sam_flippedp' definition 'sam_flippedp_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/output.h:33:57: note: Function 'Output_setup' argument 14 names different: declaration 'sam_flippedp' definition 'sam_flippedp_in'.
gmap-2025-07-31/src/output.c:85:57: note: Function 'Output_setup' argument 14 names different: declaration 'sam_flippedp' definition 'sam_flippedp_in'.
gmap-2025-07-31/src/pair.c:1034:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:1144:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:1237:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:1476:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:1643:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:1710:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:1972:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:2012:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:2196:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:3003:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:3333:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:4025:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:4452:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:4706:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:4843:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:4866:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:5408:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:5712:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:5861:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:6045:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:6266:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:7836:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:7883:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:8013:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:8050:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:8131:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:8226:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:8379:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:8475:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:8621:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:9845:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:9998:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/oligoindex_hr.c:19338:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/oligoindex_hr.c:20505:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/oligoindex_hr.c:30837:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/oligoindex_hr.c:31817:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pairpool.c:850:16: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
gmap-2025-07-31/src/pairpool.c:847:17: note: outer condition: path!=NULL
gmap-2025-07-31/src/pairpool.c:850:16: note: identical inner condition: path!=NULL
gmap-2025-07-31/src/pairpool.c:940:17: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
gmap-2025-07-31/src/pairpool.c:937:18: note: outer condition: pairs!=NULL
gmap-2025-07-31/src/pairpool.c:940:17: note: identical inner condition: pairs!=NULL
gmap-2025-07-31/src/pairpool.c:853:22: style: Condition 'end3_pairs!=NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/pairpool.c:943:21: style: Condition 'end5_path!=NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/pairpool.c:1043:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pairpool.c:678:37: style: Parameter 'source' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pairpool.c:980:69: style: Parameter 'querysequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pairpool.c:1068:11: style: Parameter 'genomesequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/parserange.c:186:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/parserange.c:257:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/parserange.c:305:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/parserange.c:434:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/parserange.c:599:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/parserange.c:709:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/parserange.c:83:7: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/parserange.c:84:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/parserange.c:85:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/parserange.c:102:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/parserange.c:103:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/parserange.c:104:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/parserange.c:121:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/parserange.c:123:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/parserange.c:124:17: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
gmap-2025-07-31/src/parserange.c:295:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/parserange.c:386:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/parserange.c:558:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/parserange.c:690:17: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/parserange.c:309:23: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/parserange.c:411:16: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/parserange.c:577:16: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/parserange.c:708:16: style: Condition 'coords==NULL' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/parserange.c:107:60: style: Redundant pointer operation on 'length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:112:38: style: Redundant pointer operation on 'length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:263:46: style: Redundant pointer operation on 'chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:276:46: style: Redundant pointer operation on 'chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:331:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:353:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:413:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:413:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:417:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:417:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:418:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:421:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:421:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:494:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:516:30: style: Redundant pointer operation on 'chrstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:579:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:579:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:582:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:582:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:583:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:586:46: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:586:63: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:615:24: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:615:41: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:618:24: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:618:41: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:619:52: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:622:24: style: Redundant pointer operation on 'genomicstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:622:41: style: Redundant pointer operation on 'genomiclength' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:646:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:661:34: style: Redundant pointer operation on 'chrstart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:715:50: style: Redundant pointer operation on 'revcomp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/parserange.c:29:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/parserange.c:52:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/parserange.c:75:80: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/parserange.c:249:44: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/parserange.c:249:64: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/parserange.c:682:12: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path-eval.c:1804:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/oligoindex_hr.c:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
gmap-2025-07-31/src/oligoindex_hr.c:20694:7: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2025-07-31/src/oligoindex_hr.c:32000:7: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
gmap-2025-07-31/src/oligoindex_hr.c:33876:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/oligoindex_hr.c:33911:7: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/oligoindex_hr.c:9107:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:9211:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:9315:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:9419:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:9523:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:9880:10: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/oligoindex_hr.c:11372:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:13114:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:14876:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:16660:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:18428:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:21410:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:21514:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:21617:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:21721:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:21824:67: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:22814:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:24588:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:26379:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:28163:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:29930:62: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:33074:22: style: Parameter 'inquery' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:33213:30: style: Parameter 'sumx' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:33213:41: style: Parameter 'sumxx' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:33293:45: style: Parameter 'sumx' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:33293:56: style: Parameter 'sumxx' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:33370:43: style: Parameter 'sumx' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:33370:54: style: Parameter 'sumxx' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:34126:50: style: Parameter 'coveredp' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:9071:23: warning: Shifting 32-bit value by 4294967250 bits is undefined behaviour. See condition at line 9069. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19392:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9069:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9071:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9088:24: warning: Shifting 32-bit value by 4294967282 bits is undefined behaviour. See condition at line 9086. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19392:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9086:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9088:24: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9117:23: warning: Shifting 32-bit value by 4294967250 bits is undefined behaviour. See condition at line 9115. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:20559:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9115:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9117:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9175:23: warning: Shifting 32-bit value by 4294967248 bits is undefined behaviour. See condition at line 9173. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19394:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9173:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9175:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9192:24: warning: Shifting 32-bit value by 4294967280 bits is undefined behaviour. See condition at line 9190. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19394:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9190:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9192:24: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9221:23: warning: Shifting 32-bit value by 4294967248 bits is undefined behaviour. See condition at line 9219. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:20561:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9219:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9221:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9279:23: warning: Shifting 32-bit value by 4294967246 bits is undefined behaviour. See condition at line 9277. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19396:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9277:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9279:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9296:24: warning: Shifting 32-bit value by 4294967278 bits is undefined behaviour. See condition at line 9294. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19396:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9294:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9296:24: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9325:23: warning: Shifting 32-bit value by 4294967246 bits is undefined behaviour. See condition at line 9323. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:20563:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9323:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9325:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9383:23: warning: Shifting 32-bit value by 4294967244 bits is undefined behaviour. See condition at line 9381. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19398:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9381:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9383:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9400:24: warning: Shifting 32-bit value by 4294967276 bits is undefined behaviour. See condition at line 9398. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19398:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9398:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9400:24: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9429:23: warning: Shifting 32-bit value by 4294967244 bits is undefined behaviour. See condition at line 9427. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:20565:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9427:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9429:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9487:23: warning: Shifting 32-bit value by 4294967242 bits is undefined behaviour. See condition at line 9485. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19400:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9485:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9487:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9504:24: warning: Shifting 32-bit value by 4294967274 bits is undefined behaviour. See condition at line 9502. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:19400:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9502:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9504:24: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9533:23: warning: Shifting 32-bit value by 4294967242 bits is undefined behaviour. See condition at line 9531. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:20567:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9531:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9533:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:21382:23: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 21380. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:30770:24: note: Assignment 'left_plus_length=0', assigned value is 0
gmap-2025-07-31/src/oligoindex_hr.c:30778:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
gmap-2025-07-31/src/oligoindex_hr.c:30827:77: note: Calling function 'count_9mers_rev_partial', 6th argument 'enddiscard' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:21380:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:21382:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:21399:26: warning: Shifting 32-bit value by 64 bits is undefined behaviour. See condition at line 21397. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:30770:24: note: Assignment 'left_plus_length=0', assigned value is 0
gmap-2025-07-31/src/oligoindex_hr.c:30778:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
gmap-2025-07-31/src/oligoindex_hr.c:30827:77: note: Calling function 'count_9mers_rev_partial', 6th argument 'enddiscard' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:21397:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:21399:26: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:21431:23: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 21429. [shiftTooManyBits]
gmap-2025-07-31/src/oligoindex_hr.c:31749:24: note: Assignment 'left_plus_length=0', assigned value is 0
gmap-2025-07-31/src/oligoindex_hr.c:31758:33: note: Assignment 'enddiscard=left_plus_length%32', assigned value is 0
gmap-2025-07-31/src/oligoindex_hr.c:31807:109: note: Calling function 'store_9mers_rev_partial', 9th argument 'enddiscard' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:21429:14: note: Assuming that condition 'pos<=enddiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:21431:23: note: Shift
gmap-2025-07-31/src/oligoindex_hr.c:9071:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*9)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19392:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9069:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9071:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9088:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*9)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19392:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9086:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9088:34: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9117:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*9)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:20559:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9115:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9117:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9175:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*8)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19394:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9173:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9175:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9192:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*8)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19394:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9190:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9192:34: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9221:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*8)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:20561:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9219:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9221:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9279:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*7)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19396:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9277:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9279:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9296:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*7)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19396:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9294:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9296:34: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9325:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*7)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:20563:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9323:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9325:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9383:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*6)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19398:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9381:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9383:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9400:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*6)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19398:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9398:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9400:34: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9429:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*6)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:20565:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9427:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9429:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9487:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*5)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19400:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9485:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9487:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9504:34: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(32-2*5)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:19400:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9502:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9504:34: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9533:33: warning: Either the condition 'pos>=startdiscard' is redundant or there is signed integer overflow for expression '2*pos-(64-2*5)'. [integerOverflowCond]
gmap-2025-07-31/src/oligoindex_hr.c:20567:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9531:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9533:33: note: Integer overflow
gmap-2025-07-31/src/oligoindex_hr.c:9071:33: 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-2025-07-31/src/oligoindex_hr.c:19392:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9069:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9071:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9088:34: 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-2025-07-31/src/oligoindex_hr.c:19392:84: note: Calling function 'count_9mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9086:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9088:34: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9117:33: 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-2025-07-31/src/oligoindex_hr.c:20559:116: note: Calling function 'store_9mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9115:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9117:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9175:33: 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-2025-07-31/src/oligoindex_hr.c:19394:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9173:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9175:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9192:34: 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-2025-07-31/src/oligoindex_hr.c:19394:84: note: Calling function 'count_8mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9190:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9192:34: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9221:33: 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-2025-07-31/src/oligoindex_hr.c:20561:116: note: Calling function 'store_8mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9219:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9221:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9279:33: 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-2025-07-31/src/oligoindex_hr.c:19396:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9277:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9279:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9296:34: 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-2025-07-31/src/oligoindex_hr.c:19396:84: note: Calling function 'count_7mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9294:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9296:34: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9325:33: 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-2025-07-31/src/oligoindex_hr.c:20563:116: note: Calling function 'store_7mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9323:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9325:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9383:33: 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-2025-07-31/src/oligoindex_hr.c:19398:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9381:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9383:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9400:34: 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-2025-07-31/src/oligoindex_hr.c:19398:84: note: Calling function 'count_6mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9398:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9400:34: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9429:33: 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-2025-07-31/src/oligoindex_hr.c:20565:116: note: Calling function 'store_6mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9427:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9429:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9487:33: 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-2025-07-31/src/oligoindex_hr.c:19400:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9485:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9487:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9504:34: 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-2025-07-31/src/oligoindex_hr.c:19400:84: note: Calling function 'count_5mers_fwd_partial', 5th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9502:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9504:34: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:9533:33: 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-2025-07-31/src/oligoindex_hr.c:20567:116: note: Calling function 'store_5mers_fwd_partial', 8th argument '0' value is 0
gmap-2025-07-31/src/oligoindex_hr.c:9531:14: note: Assuming that condition 'pos>=startdiscard' is not redundant
gmap-2025-07-31/src/oligoindex_hr.c:9533:33: note: Negative value is converted to an unsigned value
gmap-2025-07-31/src/oligoindex_hr.c:20495:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20497:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20499:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20501:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20503:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20686:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20688:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20690:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:1001:67: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path-eval.c:1002:45: style: Parameter 'queryrc' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/oligoindex_hr.c:20692:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:20694:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31807:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31809:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31811:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31813:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:149:15: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:150:19: style: Variable 'ref_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:397:17: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31815:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:591:34: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:660:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:671:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31992:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:731:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:742:15: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:817:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:828:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31994:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:867:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:878:17: style: Variable 'ref_nmatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:1074:16: style: Variable 'ninserts' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31996:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-eval.c:2501:21: style: Variable 'assignedp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:31998:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:32000:14: style: Variable 'chrpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/oligoindex_hr.c:33853:16: style: Unused variable: i [unusedVariable]
gmap-2025-07-31/src/path-learn.c:241:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path-print-m8.c:285:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-print-m8.c:283:17: note: substring is assigned
gmap-2025-07-31/src/path-print-m8.c:285:17: note: substring is overwritten
gmap-2025-07-31/src/path-print-m8.c:294:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-print-m8.c:292:17: note: substring is assigned
gmap-2025-07-31/src/path-print-m8.c:294:17: note: substring is overwritten
gmap-2025-07-31/src/path-print-m8.c:304:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-print-m8.c:302:17: note: substring is assigned
gmap-2025-07-31/src/path-print-m8.c:304:17: note: substring is overwritten
gmap-2025-07-31/src/path-print-m8.c:312:17: style: Variable 'substring' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-print-m8.c:310:17: note: substring is assigned
gmap-2025-07-31/src/path-print-m8.c:312:17: note: substring is overwritten
gmap-2025-07-31/src/path-print-m8.c:285:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-print-m8.c:294:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-print-m8.c:304:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-print-m8.c:312:17: style: Variable 'substring' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-print-sam.c:313:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path-print-sam.c:514:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path-print-sam.c:2344:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pair.c:6441:7: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2025-07-31/src/pair.c:9924:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2025-07-31/src/pair.c:472:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/pair.c:867:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/pair.c:880:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/pair.c:2738:31: style: Expression is always false because 'else if' condition matches previous condition at line 2736. [multiCondition]
gmap-2025-07-31/src/pair.c:7809:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:7810:12: note: Assignment 'in_intron=1'
gmap-2025-07-31/src/pair.c:7809:11: note: Condition '!in_intron' is redundant
gmap-2025-07-31/src/pair.c:7813:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:7814:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:7813:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:7861:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:7862:12: note: Assignment 'in_intron=1'
gmap-2025-07-31/src/pair.c:7861:11: note: Condition '!in_intron' is redundant
gmap-2025-07-31/src/pair.c:7865:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:7866:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:7865:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:7995:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:7996:12: note: Assignment 'in_intron=1'
gmap-2025-07-31/src/pair.c:7995:11: note: Condition '!in_intron' is redundant
gmap-2025-07-31/src/pair.c:7999:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8000:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:7999:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:8033:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8034:12: note: Assignment 'in_intron=1'
gmap-2025-07-31/src/pair.c:8033:11: note: Condition '!in_intron' is redundant
gmap-2025-07-31/src/pair.c:8037:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8038:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:8037:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:8116:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8117:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:8116:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:8211:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8212:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:8211:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:8360:11: style: The statement 'if (!in_intron) in_intron=1' is logically equivalent to 'in_intron=1'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8361:12: note: Assignment 'in_intron=1'
gmap-2025-07-31/src/pair.c:8360:11: note: Condition '!in_intron' is redundant
gmap-2025-07-31/src/pair.c:8364:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8365:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:8364:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:8459:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8460:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:8459:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:8655:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8656:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:8655:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:8748:11: style: The statement 'if (in_exon) in_exon=0' is logically equivalent to 'in_exon=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8749:10: note: Assignment 'in_exon=0'
gmap-2025-07-31/src/pair.c:8748:11: note: Condition 'in_exon' is redundant
gmap-2025-07-31/src/pair.c:8774:11: style: The statement 'if (in_exon) in_exon=0' is logically equivalent to 'in_exon=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8775:10: note: Assignment 'in_exon=0'
gmap-2025-07-31/src/pair.c:8774:11: note: Condition 'in_exon' is redundant
gmap-2025-07-31/src/pair.c:8833:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:8834:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:8833:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:9542:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:9543:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:9542:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:9590:8: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:9591:16: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:9590:8: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:9656:11: style: The statement 'if (in_intron) in_intron=0' is logically equivalent to 'in_intron=0'. [duplicateConditionalAssign]
gmap-2025-07-31/src/pair.c:9657:12: note: Assignment 'in_intron=0'
gmap-2025-07-31/src/pair.c:9656:11: note: Condition 'in_intron' is redundant
gmap-2025-07-31/src/pair.c:2010:49: style: Condition 'this->querypos-prev_querypos>1' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/pair.c:2006:26: note: Assuming that condition 'this->querypos>prev_querypos' is not redundant
gmap-2025-07-31/src/pair.c:2010:49: note: Condition 'this->querypos-prev_querypos>1' is always false
gmap-2025-07-31/src/pair.c:8818:28: style: Condition 'cdna_direction==0' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/pair.c:8810:28: note: Assuming that condition 'cdna_direction<0' is not redundant
gmap-2025-07-31/src/pair.c:8802:21: note: Assuming that condition 'cdna_direction>0' is not redundant
gmap-2025-07-31/src/pair.c:8818:28: note: Condition 'cdna_direction==0' is always true
gmap-2025-07-31/src/pair.c:943:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/pair.c:945:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/pair.c:973:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/pair.c:975:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/pair.c:1584:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/pair.c:1670:5: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/pair.c:1710:5: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/pair.c:5372:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/pair.c:5668:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/pair.c:1148:7: style: Variable 'ptr' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/pair.c:1136:9: note: ptr is assigned
gmap-2025-07-31/src/pair.c:1148:7: note: ptr is overwritten
gmap-2025-07-31/src/pair.c:1148:7: style: Variable 'ptr' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/pair.c:1138:9: note: ptr is assigned
gmap-2025-07-31/src/pair.c:1148:7: note: ptr is overwritten
gmap-2025-07-31/src/pair.c:1969:2: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/pair.c:2009:2: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/pair.c:8625:7: style: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/pair.c:2389:17: style: Redundant pointer operation on 'tokens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pair.c:5833:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pair.c:5833:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pair.c:5833:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pair.c:5836:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pair.c:5836:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pair.c:5836:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pair.c:3668:100: style:inconclusive: Function 'Pair_print_gff3' argument 6 names different: declaration 'restofheader' definition 'fasta_annotation'. [funcArgNamesDifferent]
gmap-2025-07-31/src/pair.h:161:100: note: Function 'Pair_print_gff3' argument 6 names different: declaration 'restofheader' definition 'fasta_annotation'.
gmap-2025-07-31/src/pair.c:3668:100: note: Function 'Pair_print_gff3' argument 6 names different: declaration 'restofheader' definition 'fasta_annotation'.
gmap-2025-07-31/src/pair.c:3867:46: style:inconclusive: Function 'Pair_print_bedpe' argument 2 names different: declaration 'pairs_querydir' definition 'pairarray'. [funcArgNamesDifferent]
gmap-2025-07-31/src/pair.h:176:46: note: Function 'Pair_print_bedpe' argument 2 names different: declaration 'pairs_querydir' definition 'pairarray'.
gmap-2025-07-31/src/pair.c:3867:46: note: Function 'Pair_print_bedpe' argument 2 names different: declaration 'pairs_querydir' definition 'pairarray'.
gmap-2025-07-31/src/pair.c:7851:41: style:inconclusive: Function 'Pair_array_nmatches_posttrim' argument 1 names different: declaration 'pairs' definition 'pairarray'. [funcArgNamesDifferent]
gmap-2025-07-31/src/pair.h:290:41: note: Function 'Pair_array_nmatches_posttrim' argument 1 names different: declaration 'pairs' definition 'pairarray'.
gmap-2025-07-31/src/pair.c:7851:41: note: Function 'Pair_array_nmatches_posttrim' argument 1 names different: declaration 'pairs' definition 'pairarray'.
gmap-2025-07-31/src/pair.c:8426:17: style:inconclusive: Function 'Pair_fracidentity_bounded' argument 11 names different: declaration 'pairs' definition 'ptr'. [funcArgNamesDifferent]
gmap-2025-07-31/src/pair.h:319:17: note: Function 'Pair_fracidentity_bounded' argument 11 names different: declaration 'pairs' definition 'ptr'.
gmap-2025-07-31/src/pair.c:8426:17: note: Function 'Pair_fracidentity_bounded' argument 11 names different: declaration 'pairs' definition 'ptr'.
gmap-2025-07-31/src/pair.c:628:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:646:20: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:670:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:705:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:754:10: style: Parameter 'chrstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:756:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:783:13: style: Parameter 'chrstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:785:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:814:27: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:814:44: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:814:55: style: Parameter 'chrstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:912:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:1003:36: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:1665:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:1705:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:1738:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:1752:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:1953:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:1993:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:2178:33: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:2398:21: style: Variable 'old_token' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:2438:34: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:2922:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:3255:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:3751:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:3870:19: style: Variable 'ptr0' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:4444:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:4635:19: style: Variable 'ptr0' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:4635:26: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:4729:39: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:4741:47: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:4753:43: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:4772:51: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:4791:51: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:4811:59: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:4833:39: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:4856:47: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:5166:9: style: Variable 'token' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:5210:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:5503:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:6212:9: style: Variable 'cigar_token' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:6212:60: style: Variable 'first_token' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:7225:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:7269:39: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:7362:39: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:7511:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:8766:19: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:8794:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:8863:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:8937:13: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:9009:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:9070:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:9139:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:9209:27: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/pair.c:9454:46: style: Parameter 'pairarray' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:9472:44: style: Parameter 'pairarray' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:9491:55: style: Parameter 'pairarray' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pair.c:3807:14: warning: Uninitialized variable: querypos [uninitvar]
gmap-2025-07-31/src/pair.c:3797:27: note: Assuming condition is false
gmap-2025-07-31/src/pair.c:3807:14: note: Uninitialized variable: querypos
gmap-2025-07-31/src/pair.c:5083:22: error: Uninitialized variable: last_token [legacyUninitvar]
gmap-2025-07-31/src/pair.c:951:8: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:962:8: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:980:8: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:3900:20: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:5212:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:5505:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:6441:20: style: Variable 'cigar_tokens' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:9071:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:9140:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:9210:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:9564:18: style: Variable 'this' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:9637:16: style: Variable 'this' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pair.c:9924:9: style: Variable 'pairs' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-print-alignment.c:751:21: style:inconclusive: Function 'Path_print_alignment' argument 4 names different: declaration 'shortread' definition 'queryseq'. [funcArgNamesDifferent]
gmap-2025-07-31/src/path-print-alignment.h:17:21: note: Function 'Path_print_alignment' argument 4 names different: declaration 'shortread' definition 'queryseq'.
gmap-2025-07-31/src/path-print-alignment.c:751:21: note: Function 'Path_print_alignment' argument 4 names different: declaration 'shortread' definition 'queryseq'.
gmap-2025-07-31/src/path-print-alignment.c:77:34: style: Parameter 'string' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path-print-alignment.c:94:42: style: Parameter 'nt' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path-print-alignment.c:171:26: style: Parameter 'genomic_diff' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path-fusion.c:2089:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:2357:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:2627:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:2893:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:3136:13: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:3378:13: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:3626:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:3870:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:4117:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:4357:11: style: Condition '0&&querylength-Path_eval_nmatches(&(*found_score),newpath,query_compress_fwd,query_compress_rev)>nmismatches_allowed' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-fusion.c:2088:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2089:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2356:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2357:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2626:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2627:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2892:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2893:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3135:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3136:49: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3146:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3377:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3378:49: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3388:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3523:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3599:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3625:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3626:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3767:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3843:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3869:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:3870:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4014:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4090:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4116:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4117:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4254:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4330:21: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4356:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:4357:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-trim.c:948:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-trim.c:958:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-trim.c:1004:42: style: Redundant pointer operation on 'qend_nsegments' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-trim.c:1004:61: style: Redundant pointer operation on 'qend_remainder' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-fusion.c:2929:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path-fusion.c:3174:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path-trim.c:817:26: style: Variable 'ignore_found_score' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-trim.c:817:7: style: Variable 'ignore_found_score' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-trim.c:1108:13: style: Variable 'nlow' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-trim.c:1126:15: style: Variable 'nlow' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-trim.c:1135:15: style: Variable 'nlow' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-fusion.c:3441:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-fusion.c:3685:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-fusion.c:3930:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-fusion.c:4170:21: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path.c:476:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path.c:486:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path.c:503:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path.c:534:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable num [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pathpair-eval.c:1760:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path.c:1304:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/path.c:1305:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/path.c:1334:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/path.c:1335:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/path.c:1341:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/path.c:1342:5: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/path.c:322:3: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
gmap-2025-07-31/src/path.c:338:3: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
gmap-2025-07-31/src/path.c:1124:57: style: Redundant pointer operation on 'new_pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path.c:1259:57: style: Redundant pointer operation on 'B_pathstores' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path.c:2502:22: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path.c:2522:25: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path.c:2629:22: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path.c:756:56: style:inconclusive: Function 'Path_fill_main_univdiagonal' argument 2 names different: declaration 'cumsum' definition 'indices'. [funcArgNamesDifferent]
gmap-2025-07-31/src/path.h:356:56: note: Function 'Path_fill_main_univdiagonal' argument 2 names different: declaration 'cumsum' definition 'indices'.
gmap-2025-07-31/src/path.c:756:56: note: Function 'Path_fill_main_univdiagonal' argument 2 names different: declaration 'cumsum' definition 'indices'.
gmap-2025-07-31/src/path.c:1095:30: style: Parameter 'old' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1095:48: style: Parameter 'end_old' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1097:34: style: Parameter 'end_new' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1101:16: style: Variable 'new_start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path.c:1237:21: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1237:37: style: Parameter 'end_A' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1239:21: style: Parameter 'B' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1239:37: style: Parameter 'end_B' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1243:16: style: Variable 'out_start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path.c:1287:17: style: Parameter 'rare' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1287:36: style: Parameter 'end_rare' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1288:36: style: Parameter 'end_freq' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/path.c:1290:26: style: Variable 'freq_start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path.c:1290:39: style: Variable 'out_start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path.c:411:15: style: Unused variable: altsplice [unusedVariable]
gmap-2025-07-31/src/path.c:434:15: style: Unused variable: altsplice [unusedVariable]
gmap-2025-07-31/src/path.c:1052:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path.c:1659:13: style: Unused variable: q [unusedVariable]
gmap-2025-07-31/src/path.c:1768:13: style: Unused variable: q [unusedVariable]
gmap-2025-07-31/src/path.c:1920:13: style: Unused variable: q [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:1095:21: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:1095:39: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:1164:21: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:1164:39: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:1311:55: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:1327:53: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:1403:56: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:1419:54: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair-eval.c:129:7: style: Unused variable: chopped_nmatches_a [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:129:27: style: Unused variable: chopped_nmatches_b [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:144:5: style: Unused variable: outerlength_knownp_x [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:144:27: style: Unused variable: outerlength_knownp_y [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:353:7: style: Unused variable: chopped_nmatches_a [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:353:27: style: Unused variable: chopped_nmatches_b [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:659:7: style: Unused variable: best_nmatches [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:659:22: style: Unused variable: nmatches [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:666:7: style: Unused variable: chop_qstart_L [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:666:22: style: Unused variable: chop_qend_L [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:666:35: style: Unused variable: chop_qstart_H [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:666:50: style: Unused variable: chop_qend_H [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:666:63: style: Unused variable: qstart [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:666:71: style: Unused variable: qend [unusedVariable]
gmap-2025-07-31/src/pathpair-eval.c:1906:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pathpair.c:2836:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pathpair.c:3096:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pathstore.c:90:32: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathstore.c:299:32: style: Redundant pointer operation on 'new' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathstore.c:514:41: style: Parameter 'univdiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/pbinom.c:719:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:738:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:823:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:898:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1003:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1040:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1063:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1163:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1316:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1391:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1420:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1477:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1641:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/pbinom.c:1411:12: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
gmap-2025-07-31/src/pbinom.c:140:7: style: struct member 'cheb_series_struct::order_sp' is never used. [unusedStructMember]
gmap-2025-07-31/src/pbinom.c:175:20: style: struct member 'Anonymous0::n' is never used. [unusedStructMember]
gmap-2025-07-31/src/pbinom.c:175:38: style: struct member 'Anonymous0::i' is never used. [unusedStructMember]
gmap-2025-07-31/src/pbinom.c:153:12: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pbinom.c:158:7: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/pbinom.c:165:7: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/printbuffer.c:446:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/printbuffer.c:323:17: style: Redundant pointer operation on 'output_list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:2964:7: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/pathpair.c:2969:9: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/pathpair.c:2964:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/pathpair.c:132:25: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:771:25: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:846:25: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:964:23: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:1014:25: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:1162:22: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:1173:22: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:1254:22: style: Redundant pointer operation on 'found_score_ptr_L' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:1329:22: style: Redundant pointer operation on 'found_score_ptr_H' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/pathpair.c:2992:7: style: Variable 'npaths_primary' is not assigned a value. [unassignedVariable]
gmap-2025-07-31/src/repetitive.c:908:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/repair.c:445:22: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/repair.c:48:10: style:inconclusive: Function 'Repair_new' argument 2 names different: declaration 'trstart_overhang' definition 'tstart_overhang'. [funcArgNamesDifferent]
gmap-2025-07-31/src/repair.h:44:10: note: Function 'Repair_new' argument 2 names different: declaration 'trstart_overhang' definition 'tstart_overhang'.
gmap-2025-07-31/src/repair.c:48:10: note: Function 'Repair_new' argument 2 names different: declaration 'trstart_overhang' definition 'tstart_overhang'.
gmap-2025-07-31/src/repair.c:48:36: style:inconclusive: Function 'Repair_new' argument 3 names different: declaration 'trstart_splice_distance' definition 'tstart_splice_distance'. [funcArgNamesDifferent]
gmap-2025-07-31/src/repair.h:44:37: note: Function 'Repair_new' argument 3 names different: declaration 'trstart_splice_distance' definition 'tstart_splice_distance'.
gmap-2025-07-31/src/repair.c:48:36: note: Function 'Repair_new' argument 3 names different: declaration 'trstart_splice_distance' definition 'tstart_splice_distance'.
gmap-2025-07-31/src/resulthr.c:72:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/resulthr.c:101:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/resulthr.c:239:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/saca-k.c:455:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/saca-k.c:154:33: style: Condition 'SA[h]==EMPTY' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/saca-k.c:154:23: note: Assuming that condition 'SA[h]>=0' is not redundant
gmap-2025-07-31/src/saca-k.c:154:33: note: Condition 'SA[h]==EMPTY' is always false
gmap-2025-07-31/src/saca-k.c:200:16: style: Condition 'j!=EMPTY' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/saca-k.c:200:9: note: Assuming that condition 'j<0' is not redundant
gmap-2025-07-31/src/saca-k.c:200:16: note: Condition 'j!=EMPTY' is always true
gmap-2025-07-31/src/saca-k.c:229:33: style: Condition 'SA[h]==EMPTY' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/saca-k.c:229:23: note: Assuming that condition 'SA[h]>=0' is not redundant
gmap-2025-07-31/src/saca-k.c:229:33: note: Condition 'SA[h]==EMPTY' is always false
gmap-2025-07-31/src/saca-k.c:274:18: style: Condition 'j!=EMPTY' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/saca-k.c:274:11: note: Assuming that condition 'j<0' is not redundant
gmap-2025-07-31/src/saca-k.c:274:18: note: Condition 'j!=EMPTY' is always true
gmap-2025-07-31/src/saca-k.c:341:16: style: Condition 'j!=EMPTY' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/saca-k.c:341:9: note: Assuming that condition 'j<0' is not redundant
gmap-2025-07-31/src/saca-k.c:341:16: note: Condition 'j!=EMPTY' is always true
gmap-2025-07-31/src/saca-k.c:65:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bkt [nullPointerOutOfMemory]
gmap-2025-07-31/src/saca-k.c:460:31: note: Assuming allocation function fails
gmap-2025-07-31/src/saca-k.c:460:9: note: Assignment 'bkt=(unsigned int*)malloc(sizeof(int)*K)', assigned value is 0
gmap-2025-07-31/src/saca-k.c:462:23: note: Calling function 'induceSAl0', 3rd argument 'bkt' value is 0
gmap-2025-07-31/src/saca-k.c:65:3: note: Null pointer dereference
gmap-2025-07-31/src/saca-k.c:24:32: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/saca-k.c:120:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/saca-k.c:133:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/saca-k.c:208:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/saca-k.c:282:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/samheader.c:98:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/samheader.c:288:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/samheader.c:309:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/samheader.c:256:3: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/samheader.c:258:5: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/samheader.c:256:3: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/samheader.c:81:11: style: Parameter 'fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/samheader.c:83:9: style: Variable 'write_mode' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/samheader.c:84:20: style: Variable 'suffix' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sarray-write.c:96:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sarray-write.c:647:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sarray-write.c:742:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sarray-write.c:1027:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sarray-write.c:1251:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sarray-write.c:2436:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sarray-write.c:2636:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sarray-write.c:2798:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sedgesort.c:177:73: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2025-07-31/src/sedgesort.c:238:62: style: Parameter 'array' can be declared as const array [constParameter]
gmap-2025-07-31/src/sedgesort.c:300:63: style: Parameter 'array1' can be declared as const array [constParameter]
gmap-2025-07-31/src/sedgesort.c:300:86: style: Parameter 'array2' can be declared as const array [constParameter]
gmap-2025-07-31/src/segmentpos.c:162:30: style: Parameter 'indices' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/segmentpos.c:163:33: style: Parameter 'align_strain' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/segmentpos.c:196:9: style: Parameter 'align_strain' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:706:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:705:15: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:705:15: note: Assignment 'fp=fopen(indexcompfile,"w")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:706:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:707:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:705:15: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:705:15: note: Assignment 'fp=fopen(indexcompfile,"w")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:707:12: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:743:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:740:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:740:13: note: Assignment 'fp=fopen(sasampleqfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:743:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:744:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:740:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:740:13: note: Assignment 'fp=fopen(sasampleqfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:744:10: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:784:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:784:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:785:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:785:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:786:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:786:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:787:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:787:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:788:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:788:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:791:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:791:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:793:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:783:13: note: Assignment 'fp=fopen(saindex0file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:793:10: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:807:3: warning: If resource allocation fails, then there is a possible null pointer dereference: sa_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:801:16: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:801:16: note: Assignment 'sa_fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:807:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:808:3: warning: If resource allocation fails, then there is a possible null pointer dereference: samples_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:802:21: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:802:21: note: Assignment 'samples_fp=fopen(sasamplesfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:808:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:814:5: warning: If resource allocation fails, then there is a possible null pointer dereference: sa_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:801:16: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:801:16: note: Assignment 'sa_fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:814:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:827:5: warning: If resource allocation fails, then there is a possible null pointer dereference: sa_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:801:16: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:801:16: note: Assignment 'sa_fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:827:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:845:14: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:844:17: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:844:17: note: Assignment 'fp=fopen(csaptrfiles[chari],"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:845:14: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:847:14: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:846:17: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:846:17: note: Assignment 'fp=fopen(csacompfiles[chari],"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:847:14: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1021:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1021:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1032:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1032:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1036:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1036:10: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1044:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1041:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1041:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1044:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1050:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1041:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1041:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1050:10: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1063:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1058:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1058:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1063:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1076:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1059:20: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1059:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1076:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1079:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1058:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1058:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1079:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1110:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1101:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1101:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1110:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1111:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1102:20: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1102:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1111:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1245:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1245:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1256:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1256:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1260:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1260:10: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1268:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1265:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1265:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1268:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1272:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1265:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1265:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1272:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1274:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1265:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1265:13: note: Assignment 'fp=fopen(rankfile,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1274:10: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1287:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1282:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1282:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1287:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1300:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1283:20: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1283:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"wb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1300:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1303:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1282:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1282:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1303:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1334:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1325:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1325:13: note: Assignment 'fp=fopen(rankfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1334:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:1335:5: warning: If resource allocation fails, then there is a possible null pointer dereference: permsa_fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:1326:20: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:1326:20: note: Assignment 'permsa_fp=fopen(permuted_sarray_file,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:1335:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:2317:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:2316:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:2316:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:2317:3: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:2320:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/sarray-write.c:2316:13: note: Assuming allocation function fails
gmap-2025-07-31/src/sarray-write.c:2316:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
gmap-2025-07-31/src/sarray-write.c:2320:5: note: Null pointer dereference
gmap-2025-07-31/src/sarray-write.c:3020:12: style: Variable 'plcpcomp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/sarray-write.c:3019:12: note: plcpcomp is assigned
gmap-2025-07-31/src/sarray-write.c:3020:12: note: plcpcomp is overwritten
gmap-2025-07-31/src/sarray-write.c:3083:9: style: Variable 'lcp_i' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/sarray-write.c:3033:9: note: lcp_i is assigned
gmap-2025-07-31/src/sarray-write.c:3083:9: note: lcp_i is overwritten
gmap-2025-07-31/src/sarray-write.c:82:27: style: Parameter 'sarrayfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:87:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sarray-write.c:264:74: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:265:54: style: Parameter 'SA' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:723:66: style: Parameter 'sasampleqfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:723:87: style: Parameter 'sasamplesfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:723:108: style: Parameter 'saindex0file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:725:21: style: Variable 'SA_inv' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sarray-write.c:998:44: style: Parameter 'rankfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:998:60: style: Parameter 'permuted_sarray_file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:1001:10: style: Variable 'SA' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sarray-write.c:1006:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sarray-write.c:1220:12: style: Parameter 'rankfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:1220:28: style: Parameter 'permuted_sarray_file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:1225:10: style: Variable 'SA' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sarray-write.c:1230:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sarray-write.c:2296:51: style: Parameter 'sarrayfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sarray-write.c:2998:10: style: Variable 'SA' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/semaphore.c:22:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IPC_CREAT [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/semaphore.c:40:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/semaphore.c:56:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SETVAL [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/semaphore.c:82:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEM_UNDO [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/semaphore.c:95:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEM_UNDO [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/semaphore.c:83:3: warning: Return value of function semop() is not used. [ignoredReturnValue]
gmap-2025-07-31/src/semaphore.c:96:3: warning: Return value of function semop() is not used. [ignoredReturnValue]
gmap-2025-07-31/src/semaphore.c:14:49: style:inconclusive: Function 'Semaphore_create' argument 3 names different: declaration 'vals' definition 'values'. [funcArgNamesDifferent]
gmap-2025-07-31/src/semaphore.h:20:49: note: Function 'Semaphore_create' argument 3 names different: declaration 'vals' definition 'values'.
gmap-2025-07-31/src/semaphore.c:14:49: note: Function 'Semaphore_create' argument 3 names different: declaration 'vals' definition 'values'.
gmap-2025-07-31/src/semaphore.c:17:9: style: union member 'semun::val' is never used. [unusedStructMember]
gmap-2025-07-31/src/semaphore.c:18:22: style: union member 'semun::buf' is never used. [unusedStructMember]
gmap-2025-07-31/src/semaphore.c:51:22: style: union member 'semun::buf' is never used. [unusedStructMember]
gmap-2025-07-31/src/semaphore.c:52:13: style: union member 'semun::array' is never used. [unusedStructMember]
gmap-2025-07-31/src/semaphore.c:80:14: style: Variable 'op.sem_num' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/semaphore.c:81:13: style: Variable 'op.sem_op' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/semaphore.c:82:14: style: Variable 'op.sem_flg' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/semaphore.c:93:14: style: Variable 'op.sem_num' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/semaphore.c:94:13: style: Variable 'op.sem_op' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/semaphore.c:95:14: style: Variable 'op.sem_flg' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/sequence.c:543:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sequence.c:813:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sequence.c:915:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sequence.c:1411:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sequence.c:1579:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sequence.c:1704:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sequence.c:1926:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:273:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:401:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:699:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:1020:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:1164:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:2713:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:3514:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:3869:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:4552:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:4573:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:4590:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:4606:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:4618:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:5275:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/shortread.c:5321:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/sequence.c:641:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/sequence.c:649:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/sequence.c:717:7: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/sequence.c:720:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/sequence.c:851:2: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/sequence.c:865:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/sequence.c:868:4: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/sequence.c:875:18: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/sequence.c:949:2: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/sequence.c:962:14: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/sequence.c:965:4: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/sequence.c:972:18: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/sequence.c:2156:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/sequence.c:1731:24: style: Expression is always true because 'else if' condition is opposite to previous condition at line 1720. [multiCondition]
gmap-2025-07-31/src/sequence.c:1720:24: note: first condition
gmap-2025-07-31/src/sequence.c:1731:24: note: else if condition is opposite to first condition
gmap-2025-07-31/src/sequence.c:1040:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1046:36: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1046:49: style: Redundant pointer operation on 'pointer2a' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1046:63: style: Redundant pointer operation on 'length2a' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1047:8: style: Redundant pointer operation on 'pointer2b' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1047:22: style: Redundant pointer operation on 'length2b' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1465:36: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1537:37: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:1607:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/sequence.c:165:18: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sequence.c:179:18: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sequence.c:679:9: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sequence.c:1108:24: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sequence.c:1121:21: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sequence.c:1299:23: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/sequence.c:1304:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2025-07-31/src/sequence.c:1699:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/sequence.c:1869:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2025-07-31/src/sequence.c:1908:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2025-07-31/src/sequence.c:1964:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2025-07-31/src/sequence.c:2010:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2025-07-31/src/path-solve.c:2856:11: style: Condition '1||newpaths==NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:2932:20: style: Condition '0&&medial_splice_trimpos_0==Intlist_head(path->endpoints)' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:3294:11: style: Condition '1||newpaths==NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:3371:20: style: Condition '0&&medial_splice_trimpos_0==Intlist_head(path->endpoints)' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:3778:9: style: Condition '1||qstart_sense_paths==NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:3837:11: style: Condition '1||qstart_antisense_paths==NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:3904:9: style: Condition '1||qend_sense_paths==NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:3966:11: style: Condition '1||qend_antisense_paths==NULL' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:4384:9: style: Condition '0&&qstart<=8' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/path-solve.c:2329:13: style: Variable 'qend1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:2289:13: note: qend1 is assigned
gmap-2025-07-31/src/path-solve.c:2329:13: note: qend1 is overwritten
gmap-2025-07-31/src/path-solve.c:2328:15: style: Variable 'qstart1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:2290:15: note: qstart1 is assigned
gmap-2025-07-31/src/path-solve.c:2328:15: note: qstart1 is overwritten
gmap-2025-07-31/src/path-solve.c:2333:15: style: Variable 'qstart2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:2292:15: note: qstart2 is assigned
gmap-2025-07-31/src/path-solve.c:2333:15: note: qstart2 is overwritten
gmap-2025-07-31/src/path-solve.c:2334:13: style: Variable 'qend2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:2293:13: note: qend2 is assigned
gmap-2025-07-31/src/path-solve.c:2334:13: note: qend2 is overwritten
gmap-2025-07-31/src/path-solve.c:4437:12: style: Variable 'auxinfo->qstart' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:4373:10: note: qstart is assigned 'auxinfo->qstart' here.
gmap-2025-07-31/src/path-solve.c:4437:12: note: Variable 'auxinfo->qstart' is assigned an expression that holds the same value.
gmap-2025-07-31/src/path-solve.c:5470:20: style: Variable 'new_univdiagonal' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:4849:19: note: new_univdiagonal is assigned
gmap-2025-07-31/src/path-solve.c:5470:20: note: new_univdiagonal is overwritten
gmap-2025-07-31/src/path-solve.c:5470:20: style: Variable 'new_univdiagonal' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:5314:19: note: new_univdiagonal is assigned
gmap-2025-07-31/src/path-solve.c:5470:20: note: new_univdiagonal is overwritten
gmap-2025-07-31/src/path-solve.c:5470:20: style: Variable 'new_univdiagonal' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:5412:21: note: new_univdiagonal is assigned
gmap-2025-07-31/src/path-solve.c:5470:20: note: new_univdiagonal is overwritten
gmap-2025-07-31/src/path-solve.c:6460:20: style: Variable 'new_univdiagonal' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:5814:19: note: new_univdiagonal is assigned
gmap-2025-07-31/src/path-solve.c:6460:20: note: new_univdiagonal is overwritten
gmap-2025-07-31/src/path-solve.c:6460:20: style: Variable 'new_univdiagonal' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:6296:19: note: new_univdiagonal is assigned
gmap-2025-07-31/src/path-solve.c:6460:20: note: new_univdiagonal is overwritten
gmap-2025-07-31/src/path-solve.c:6460:20: style: Variable 'new_univdiagonal' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/path-solve.c:6398:21: note: new_univdiagonal is assigned
gmap-2025-07-31/src/path-solve.c:6460:20: note: new_univdiagonal is overwritten
gmap-2025-07-31/src/path-solve.c:2607:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:3101:25: style: Redundant pointer operation on 'qstart_paths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:3550:23: style: Redundant pointer operation on 'qend_paths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:3614:32: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4017:52: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4046:56: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4125:48: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4168:48: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4290:36: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4304:36: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4441:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4443:10: style: Redundant pointer operation on 'unextended_sense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4443:37: style: Redundant pointer operation on 'unextended_antisense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4444:10: style: Redundant pointer operation on 'sense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4444:26: style: Redundant pointer operation on 'antisense_paths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4484:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4490:46: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4602:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4618:34: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4633:36: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:5591:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:6597:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:7530:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-solve.c:4673:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path-solve.c:5627:16: style: Variable 'new_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path-solve.c:783:14: style: Variable 'low_left' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-solve.c:590:7: style: Unused variable: type [unusedVariable]
gmap-2025-07-31/src/path-solve.c:590:13: style: Unused variable: typei [unusedVariable]
gmap-2025-07-31/src/path-solve.c:590:20: style: Unused variable: typej [unusedVariable]
gmap-2025-07-31/src/path-solve.c:591:27: style: Unused variable: splice_qpos [unusedVariable]
gmap-2025-07-31/src/path-solve.c:591:40: style: Unused variable: splice_qpos_i [unusedVariable]
gmap-2025-07-31/src/path-solve.c:591:55: style: Unused variable: splice_qpos_j [unusedVariable]
gmap-2025-07-31/src/path-solve.c:591:70: style: Unused variable: trimpos5 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:591:80: style: Unused variable: trimpos3 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:592:15: style: Unused variable: middle_univdiagonal [unusedVariable]
gmap-2025-07-31/src/path-solve.c:593:12: style: Unused variable: splice_distance [unusedVariable]
gmap-2025-07-31/src/path-solve.c:593:29: style: Unused variable: splice_distance_i [unusedVariable]
gmap-2025-07-31/src/path-solve.c:593:48: style: Unused variable: splice_distance_j [unusedVariable]
gmap-2025-07-31/src/path-solve.c:594:10: style: Unused variable: donor1_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:594:23: style: Unused variable: acceptor1_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:594:39: style: Unused variable: donor2_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:594:52: style: Unused variable: acceptor2_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:596:37: style: Unused variable: nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:597:43: style: Unused variable: ref_nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:598:35: style: Unused variable: nmismatches_middle [unusedVariable]
gmap-2025-07-31/src/path-solve.c:598:55: style: Unused variable: ref_nmismatches_middle [unusedVariable]
gmap-2025-07-31/src/path-solve.c:599:39: style: Unused variable: cont_ref_nmismatches [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1699:10: style: Variable 'left' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-solve.c:1487:7: style: Unused variable: type [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1487:13: style: Unused variable: typei [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1487:20: style: Unused variable: typej [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1488:27: style: Unused variable: splice_qpos [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1488:40: style: Unused variable: splice_qpos_i [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1488:55: style: Unused variable: splice_qpos_j [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1488:70: style: Unused variable: trimpos5 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1488:80: style: Unused variable: trimpos3 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1489:15: style: Unused variable: middle_univdiagonal [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1490:12: style: Unused variable: splice_distance [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1490:29: style: Unused variable: splice_distance_i [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1490:48: style: Unused variable: splice_distance_j [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1491:10: style: Unused variable: donor1_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1491:23: style: Unused variable: acceptor1_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1491:39: style: Unused variable: donor2_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1491:52: style: Unused variable: acceptor2_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1493:37: style: Unused variable: nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1494:43: style: Unused variable: ref_nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1495:35: style: Unused variable: nmismatches_middle [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1495:55: style: Unused variable: ref_nmismatches_middle [unusedVariable]
gmap-2025-07-31/src/path-solve.c:1496:39: style: Unused variable: cont_ref_nmismatches [unusedVariable]
gmap-2025-07-31/src/path-solve.c:2410:12: style: Variable 'ninserts2' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-solve.c:2738:22: style: Variable 'qstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-solve.c:3174:20: style: Variable 'qend' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-solve.c:4674:19: style: Unused variable: middle_univdiagonal [unusedVariable]
gmap-2025-07-31/src/path-solve.c:4687:7: style: Unused variable: type [unusedVariable]
gmap-2025-07-31/src/path-solve.c:4688:46: style: Unused variable: trimpos3 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:4691:25: style: Unused variable: cont_ref_nmismatches [unusedVariable]
gmap-2025-07-31/src/path-solve.c:4692:35: style: Unused variable: nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:4693:45: style: Unused variable: ref_nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:5628:19: style: Unused variable: middle_univdiagonal [unusedVariable]
gmap-2025-07-31/src/path-solve.c:5641:7: style: Unused variable: type [unusedVariable]
gmap-2025-07-31/src/path-solve.c:5642:36: style: Unused variable: trimpos5 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:5645:25: style: Unused variable: cont_ref_nmismatches [unusedVariable]
gmap-2025-07-31/src/path-solve.c:5646:35: style: Unused variable: nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:5647:45: style: Unused variable: ref_nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7159:24: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-solve.c:7130:37: style: Unused variable: nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7131:43: style: Unused variable: ref_nmismatches_indel [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7133:10: style: Unused variable: donor_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7133:22: style: Unused variable: acceptor_prob [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7135:7: style: Unused variable: type [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7136:7: style: Unused variable: trimpos5 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7136:17: style: Unused variable: trimpos3 [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7136:27: style: Unused variable: supporti [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7136:37: style: Unused variable: supportj [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7137:7: style: Unused variable: splice_qpos [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7138:47: style: Unused variable: univdiagonal_k [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7139:5: style: Unused variable: segmenti_left [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7139:20: style: Unused variable: segmentj_left [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7140:12: style: Unused variable: splice_distance [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7142:7: style: Unused variable: ignore [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7148:10: style: Unused variable: j [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7149:16: style: Unused variable: r [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7149:19: style: Unused variable: s [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7151:14: style: Unused variable: splice_junction [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7151:31: style: Unused variable: indel_junction [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7156:46: style: Unused variable: p [unusedVariable]
gmap-2025-07-31/src/path-solve.c:7159:8: style: Variable 'sense_forward_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/simplepair.c:68:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:73:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:169:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:721:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:1013:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:1199:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:1489:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:1512:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:1546:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:1763:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/single-cell.c:65:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/single-cell.c:161:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/single-cell.c:351:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/single-cell.c:711:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/single-cell.c:74:7: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/single-cell.c:77:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/single-cell.c:135:8: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/single-cell.c:179:2: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/single-cell.c:187:23: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/single-cell.c:682:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/single-cell.c:674:13: note: Assuming allocation function fails
gmap-2025-07-31/src/single-cell.c:674:13: note: Assignment 'fp=fopen(whitelist_file,"r")', assigned value is 0
gmap-2025-07-31/src/single-cell.c:682:10: note: Null pointer dereference
gmap-2025-07-31/src/single-cell.c:392:45: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:398:21: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:404:39: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:404:52: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:409:16: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:412:18: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:412:31: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:625:39: style: Redundant pointer operation on 'whitelist_total' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:626:11: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:626:24: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:626:36: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:627:30: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:627:40: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/single-cell.c:63:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/single-cell.c:132:34: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/single-cell.c:634:9: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/single-cell.c:635:9: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/single-cell.c:657:35: style: Parameter 'whitelist_file' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/single-cell.c:776:50: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/single-cell.c:776:66: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/single-cell.c:857:16: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/single-cell.c:404:23: style: Variable 'fulllength' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/shortread.c:412:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/shortread.c:420:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/shortread.c:710:19: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/shortread.c:718:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/shortread.c:1029:7: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/shortread.c:1032:5: style: Obsolescent function 'rindex' called. It is recommended to use 'strrchr' instead. [prohibitedrindexCalled]
gmap-2025-07-31/src/shortread.c:1133:8: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/shortread.c:1187:4: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/shortread.c:1198:23: style: Obsolescent function 'index' called. It is recommended to use 'strchr' instead. [prohibitedindexCalled]
gmap-2025-07-31/src/shortread.c:5285:17: style: Condition 'shift==0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/shortread.c:5331:17: style: Condition 'shift==0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/shortread.c:2446:12: portability: Casting non-zero decimal integer literal to pointer. [intToPointerCast]
gmap-2025-07-31/src/shortread.c:2966:24: portability: Casting non-zero decimal integer literal to pointer. [intToPointerCast]
gmap-2025-07-31/src/shortread.c:2967:9: portability: Casting non-zero decimal integer literal to pointer. [intToPointerCast]
gmap-2025-07-31/src/shortread.c:4041:22: portability: Casting non-zero decimal integer literal to pointer. [intToPointerCast]
gmap-2025-07-31/src/shortread.c:4042:14: portability: Casting non-zero decimal integer literal to pointer. [intToPointerCast]
gmap-2025-07-31/src/shortread.c:2769:45: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2775:29: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2787:45: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2787:58: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2797:40: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2797:53: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2802:16: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2805:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2805:48: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2816:35: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2816:48: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2844:42: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2856:29: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2870:55: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2881:20: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2884:39: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2884:52: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2905:20: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2908:50: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2941:18: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2944:37: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:2944:50: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3924:42: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3932:45: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3938:35: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3945:39: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3945:52: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3960:14: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3963:33: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3963:46: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:3983:37: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4006:45: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4021:16: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4024:46: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4462:44: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4462:57: style: Redundant pointer operation on 'queryseq2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4462:71: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4463:28: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4463:38: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4488:38: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4488:51: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4488:63: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4488:75: style: Redundant pointer operation on 'queryseq2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4489:10: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4489:21: style: Redundant pointer operation on 'input2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4489:51: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4489:61: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4518:38: style: Redundant pointer operation on 'nextchar' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4518:51: style: Redundant pointer operation on 'nchars1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4518:63: style: Redundant pointer operation on 'nchars2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4518:75: style: Redundant pointer operation on 'queryseq2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4519:10: style: Redundant pointer operation on 'input1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4519:21: style: Redundant pointer operation on 'input2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4519:51: style: Redundant pointer operation on 'files' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:4519:61: style: Redundant pointer operation on 'nfiles' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:368:9: style:inconclusive: Function 'Shortread_setup' argument 3 names different: declaration 'force_singled_end_p_in' definition 'force_single_end_p_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/shortread.h:25:9: note: Function 'Shortread_setup' argument 3 names different: declaration 'force_singled_end_p_in' definition 'force_single_end_p_in'.
gmap-2025-07-31/src/shortread.c:368:9: note: Function 'Shortread_setup' argument 3 names different: declaration 'force_singled_end_p_in' definition 'force_single_end_p_in'.
gmap-2025-07-31/src/smooth.c:128:34: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:129:35: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:130:36: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:193:35: style: Redundant pointer operation on 'nexons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:299:36: style: Redundant pointer operation on 'nintrons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:332:38: style: Redundant pointer operation on 'nintrons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:333:41: style: Redundant pointer operation on 'nintrons' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:959:36: style: Redundant pointer operation on 'deletep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:1045:34: style: Redundant pointer operation on 'shortp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/smooth.c:1199:34: style: Redundant pointer operation on 'badp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/shortread.c:396:26: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:693:23: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:1018:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:1130:34: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/shortread.c:1438:24: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/shortread.c:1469:21: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/shortread.c:1486:23: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/shortread.c:1491:8: style: Variable 'uppercaseCode' can be declared as const array [constVariable]
gmap-2025-07-31/src/shortread.c:2116:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:2214:9: style: Variable 'contents1' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:2215:9: style: Variable 'contents2' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:2310:9: style: Variable 'contents1' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:2311:9: style: Variable 'contents2' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:2376:9: style: Variable 'contents1' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:2377:9: style: Variable 'contents2' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/shortread.c:3501:70: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/smooth.c:391:60: style: Parameter 'intronlengths' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:427:70: style: Parameter 'exonmatches' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:475:15: style: Parameter 'exonmatches' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:475:33: style: Parameter 'exonprotects' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:476:15: style: Parameter 'intronlengths' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:589:66: style: Parameter 'exonmatches' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:590:16: style: Parameter 'donor_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:590:37: style: Parameter 'acceptor_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:591:13: style: Parameter 'intron_matches_left' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:591:39: style: Parameter 'intron_denominator_left' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:592:13: style: Parameter 'intron_matches_right' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:592:40: style: Parameter 'intron_denominator_right' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/smooth.c:746:15: style: Parameter 'exonstatus' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:157:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:220:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:240:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:380:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:730:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:941:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:1172:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:1292:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:1383:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/snpindex.c:1919:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/simplepair.c:1356:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2025-07-31/src/simplepair.c:1827:14: style: Condition 'chrnum!=0' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/simplepair.c:138:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/simplepair.c:685:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/simplepair.c:969:6: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
gmap-2025-07-31/src/simplepair.c:394:17: style: Redundant pointer operation on 'tokens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/simplepair.c:1128:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/simplepair.c:1128:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/simplepair.c:1128:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/simplepair.c:1131:35: style: Redundant pointer operation on 'intronp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/simplepair.c:1131:47: style: Redundant pointer operation on 'hardclip_start' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/simplepair.c:1131:66: style: Redundant pointer operation on 'hardclip_end' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/simplepair.c:1748:16: style: Local variable 'flag' shadows outer argument [shadowArgument]
gmap-2025-07-31/src/simplepair.c:1738:45: note: Shadowed declaration
gmap-2025-07-31/src/simplepair.c:1748:16: note: Shadow variable
gmap-2025-07-31/src/simplepair.c:377:34: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:417:9: style: Variable 'token' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/simplepair.c:529:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/simplepair.c:810:19: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/simplepair.c:1145:9: style: Variable 'cigar_token' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/simplepair.c:1145:60: style: Variable 'first_token' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/simplepair.c:1375:39: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:1387:47: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:1399:43: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:1418:51: style: Parameter 'contents' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:1437:51: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:1457:59: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:1479:39: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:1502:47: style: Parameter 'quality' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/simplepair.c:446:22: error: Uninitialized variable: last_token [legacyUninitvar]
gmap-2025-07-31/src/simplepair.c:347:14: style: Variable 'highpair' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/simplepair.c:362:14: style: Variable 'highpair' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/simplepair.c:531:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/simplepair.c:812:29: style: Variable 'exon_genomestart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/simplepair.c:1356:18: style: Variable 'cigar_tokens' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/snpindex.c:1495:3: style: Obsolescent function 'bcopy' called. It is recommended to use 'memcpy' or 'memmove' instead. [prohibitedbcopyCalled]
gmap-2025-07-31/src/snpindex.c:1830:23: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2025-07-31/src/snpindex.c:1826:23: note: First condition
gmap-2025-07-31/src/snpindex.c:1830:23: note: Second condition
gmap-2025-07-31/src/snpindex.c:211:44: style: Parameter 'divstring' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:321:9: style: Variable 'snptype' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:676:45: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:689:22: style: Parameter 'output_offsetsmetafile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:689:52: style: Parameter 'output_offsetsstrmfile' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:1084:86: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:1087:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:1119:27: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:1119:55: style: Parameter 'end2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:1123:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:1123:26: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:1229:61: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:1230:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:1252:61: style: Parameter 'end1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:1253:27: style: Parameter 'end2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/snpindex.c:1254:10: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:1254:26: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:1336:28: style: Variable 'destdir' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/snpindex.c:312:15: style: Unused variable: centerp [unusedVariable]
gmap-2025-07-31/src/snpindex.c:893:16: style: Variable 'buffer_i' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/snpindex.c:1367:7: style: Unused variable: ref_offsetsmeta_fd [unusedVariable]
gmap-2025-07-31/src/snpindex.c:1367:27: style: Unused variable: ref_offsetsstrm_fd [unusedVariable]
gmap-2025-07-31/src/snpindex.c:1367:47: style: Unused variable: ref_positions_high_fd [unusedVariable]
gmap-2025-07-31/src/snpindex.c:1367:70: style: Unused variable: ref_positions_fd [unusedVariable]
gmap-2025-07-31/src/snpindex.c:1368:5: style: Unused variable: snponly_offsetsmeta_fd [unusedVariable]
gmap-2025-07-31/src/snpindex.c:1368:29: style: Unused variable: snponly_offsetsstrm_fd [unusedVariable]
gmap-2025-07-31/src/spliceendsgen.c:113:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/spliceendsgen.c:147:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/spliceends.c:739:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable univdiagonal [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/spliceends.c:2889:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/spliceends.c:3097:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable univdiagonal [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/spliceends.c:5016:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/path-print-sam.c:776:17: style: Redundant pointer operation on 'hardclip_low' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:776:34: style: Redundant pointer operation on 'hardclip_high' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2048:20: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2059:20: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2184:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2195:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2302:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2313:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2356:25: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2367:25: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2417:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2428:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2463:25: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2478:25: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2552:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2564:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2588:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2624:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2664:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2692:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2732:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2760:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2869:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2884:22: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2927:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:2938:24: style: Redundant pointer operation on 'fp_failedinput_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:3002:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:3013:22: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:3056:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:3067:24: style: Redundant pointer operation on 'fp_failedinput_2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/path-print-sam.c:1869:37: style:inconclusive: Function 'Path_print_sam' argument 16 names different: declaration 'queryseq_mate' definition 'mate_queryseq'. [funcArgNamesDifferent]
gmap-2025-07-31/src/path-print-sam.h:32:37: note: Function 'Path_print_sam' argument 16 names different: declaration 'queryseq_mate' definition 'mate_queryseq'.
gmap-2025-07-31/src/path-print-sam.c:1869:37: note: Function 'Path_print_sam' argument 16 names different: declaration 'queryseq_mate' definition 'mate_queryseq'.
gmap-2025-07-31/src/path-print-sam.c:762:16: style: Variable 'alts_univdiagonals' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/path-print-sam.c:2490:30: error: Uninitialized variable: npaths1_primary [legacyUninitvar]
gmap-2025-07-31/src/path-print-sam.c:2490:48: error: Uninitialized variable: npaths1_altloc [legacyUninitvar]
gmap-2025-07-31/src/path-print-sam.c:2491:6: error: Uninitialized variable: npaths2_primary [legacyUninitvar]
gmap-2025-07-31/src/path-print-sam.c:2491:24: error: Uninitialized variable: npaths2_altloc [legacyUninitvar]
gmap-2025-07-31/src/path-print-sam.c:2182:41: error: Uninitialized variable: clipdir [legacyUninitvar]
gmap-2025-07-31/src/path-print-sam.c:216:14: style: Variable 'ninserts' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-print-sam.c:421:12: style: Variable 'ninserts' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/path-print-sam.c:762:36: style: Unused variable: medial_univdiagonal [unusedVariable]
gmap-2025-07-31/src/path-print-sam.c:764:15: style: Unused variable: chroffset [unusedVariable]
gmap-2025-07-31/src/path-print-sam.c:1128:15: style: Unused variable: chroffset [unusedVariable]
gmap-2025-07-31/src/path-print-sam.c:1367:15: style: Unused variable: chroffset [unusedVariable]
gmap-2025-07-31/src/splicetrie_build.c:424:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:852:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:1395:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:1556:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:2042:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:2383:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:2804:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:3111:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:3382:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splicetrie_build.c:770:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/splicetrie_build.c:1585:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie_build.c:1588:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie_build.c:1591:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie_build.c:1594:40: style: Redundant pointer operation on 'nprinted' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie_build.c:189:34: style: Parameter 'buffer' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:237:35: style: Parameter 'buffer' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:383:54: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:804:50: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:1858:22: style: Parameter 'splicesites' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:1858:49: style: Parameter 'splicetypes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:1859:19: style: Parameter 'splicedists' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:2061:13: style: Parameter 'nsplicepartners_skip' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:2061:40: style: Parameter 'nsplicepartners_obs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:2061:66: style: Parameter 'nsplicepartners_max' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:2062:22: style: Parameter 'splicetypes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:2863:58: style: Parameter 'splicesites' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:2863:85: style: Parameter 'splicetypes' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:2865:56: style: Parameter 'splicing_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splicetrie_build.c:1281:18: style: struct member 'Trie_T::leaf' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1283:7: style: struct member 'Trie_T::nsites' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1284:7: style: struct member 'Trie_T::na' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1285:7: style: struct member 'Trie_T::nc' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1286:7: style: struct member 'Trie_T::ng' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1287:7: style: struct member 'Trie_T::nt' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1289:10: style: struct member 'Trie_T::triea' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1290:10: style: struct member 'Trie_T::triec' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1291:10: style: struct member 'Trie_T::trieg' is never used. [unusedStructMember]
gmap-2025-07-31/src/splicetrie_build.c:1292:10: style: struct member 'Trie_T::triet' is never used. [unusedStructMember]
gmap-2025-07-31/src/stage1.c:3378:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/splice.c:7228:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/splice.c:7250:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/splice.c:7228:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/splice.c:7507:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/splice.c:7528:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/splice.c:7507:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/splice.c:3817:19: style: Variable 'best_splice_qpos' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/splice.c:3768:20: note: best_splice_qpos is assigned
gmap-2025-07-31/src/splice.c:3817:19: note: best_splice_qpos is overwritten
gmap-2025-07-31/src/splice.c:5090:19: style: Variable 'best_splice_qpos' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/splice.c:5041:20: note: best_splice_qpos is assigned
gmap-2025-07-31/src/splice.c:5090:19: note: best_splice_qpos is overwritten
gmap-2025-07-31/src/splice.c:6258:19: style: Variable 'best_splice_qpos' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/splice.c:6222:20: note: best_splice_qpos is assigned
gmap-2025-07-31/src/splice.c:6258:19: note: best_splice_qpos is overwritten
gmap-2025-07-31/src/splice.c:1589:3: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
gmap-2025-07-31/src/splice.c:1030:24: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1030:35: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1032:27: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1032:41: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1164:27: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1164:41: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1166:24: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1166:35: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1316:24: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1316:35: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1318:27: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1318:41: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1467:27: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1467:41: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1469:24: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:1469:35: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:2436:42: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:2448:40: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:2461:42: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:2476:40: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6245:59: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6245:79: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6246:13: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6246:41: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6247:13: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6247:45: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6267:59: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6267:79: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6268:13: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6268:41: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6269:13: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6269:45: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6291:63: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6291:83: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6292:10: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6292:38: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6293:10: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6293:42: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6313:63: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6313:83: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6314:10: style: Redundant pointer operation on 'best_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6314:38: style: Redundant pointer operation on 'best_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6315:10: style: Redundant pointer operation on 'best_ref_nmismatches_j' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:6315:42: style: Redundant pointer operation on 'best_ref_nmismatches_i' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7199:18: style: Redundant pointer operation on 'best_type' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7199:32: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7199:43: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7199:54: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7199:68: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7199:82: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7199:102: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7200:9: style: Redundant pointer operation on 'best_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7200:37: style: Redundant pointer operation on 'best_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7201:9: style: Redundant pointer operation on 'best_ref_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7201:41: style: Redundant pointer operation on 'best_ref_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7478:22: style: Redundant pointer operation on 'best_type' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7478:36: style: Redundant pointer operation on 'donor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7478:47: style: Redundant pointer operation on 'donor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7478:58: style: Redundant pointer operation on 'acceptor1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7478:72: style: Redundant pointer operation on 'acceptor2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7478:86: style: Redundant pointer operation on 'best_donor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7478:106: style: Redundant pointer operation on 'best_acceptor_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7479:13: style: Redundant pointer operation on 'best_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7479:41: style: Redundant pointer operation on 'best_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7480:13: style: Redundant pointer operation on 'best_ref_nmismatches_A' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:7480:45: style: Redundant pointer operation on 'best_ref_nmismatches_D' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splice.c:270:11: style:inconclusive: Function 'Splice_accept_p' argument 3 names different: declaration 'splice_prob_1' definition 'splice_prob_i'. [funcArgNamesDifferent]
gmap-2025-07-31/src/splice.h:80:11: note: Function 'Splice_accept_p' argument 3 names different: declaration 'splice_prob_1' definition 'splice_prob_i'.
gmap-2025-07-31/src/splice.c:270:11: note: Function 'Splice_accept_p' argument 3 names different: declaration 'splice_prob_1' definition 'splice_prob_i'.
gmap-2025-07-31/src/splice.c:270:33: style:inconclusive: Function 'Splice_accept_p' argument 4 names different: declaration 'splice_prob_2' definition 'splice_prob_j'. [funcArgNamesDifferent]
gmap-2025-07-31/src/splice.h:80:33: note: Function 'Splice_accept_p' argument 4 names different: declaration 'splice_prob_2' definition 'splice_prob_j'.
gmap-2025-07-31/src/splice.c:270:33: note: Function 'Splice_accept_p' argument 4 names different: declaration 'splice_prob_2' definition 'splice_prob_j'.
gmap-2025-07-31/src/splice.c:415:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/splice.c:514:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/splice.c:613:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/splice.c:710:16: style: Variable 'endpoints' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/splice.c:856:23: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:861:24: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:924:13: style: Parameter 'segmentD_types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:924:34: style: Parameter 'segmentA_types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:925:16: style: Parameter 'segmentD_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:925:40: style: Parameter 'segmentA_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1059:10: style: Parameter 'segmentA_types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1059:31: style: Parameter 'segmentD_types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1060:13: style: Parameter 'segmentA_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1060:37: style: Parameter 'segmentD_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1544:18: style: Parameter 'middle_univdiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1959:13: style: Parameter 'segmenti_sites' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1959:34: style: Parameter 'segmentj_sites' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1959:55: style: Parameter 'segmenti_types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1959:76: style: Parameter 'segmentj_types' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1960:16: style: Parameter 'segmenti_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1960:40: style: Parameter 'segmentj_probs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/splice.c:1315:7: warning: Uninitialized variable: best_splice_querypos [uninitvar]
gmap-2025-07-31/src/splice.c:1261:63: note: Assuming condition is false
gmap-2025-07-31/src/splice.c:1315:7: note: Uninitialized variable: best_splice_querypos
gmap-2025-07-31/src/splice.c:1466:7: warning: Uninitialized variable: best_splice_querypos [uninitvar]
gmap-2025-07-31/src/splice.c:1413:63: note: Assuming condition is false
gmap-2025-07-31/src/splice.c:1466:7: note: Uninitialized variable: best_splice_querypos
gmap-2025-07-31/src/splice.c:277:8: style: Unused variable: acceptp [unusedVariable]
gmap-2025-07-31/src/splice.c:1562:40: style: Variable 'best_middle_univdiagonal' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:1565:24: style: Variable 'best_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:1990:13: style: Variable 'best_prob' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:2104:13: style: Variable 'best_prob' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:2178:13: style: Variable 'best_prob' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:2312:13: style: Variable 'best_prob' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:2387:13: style: Variable 'best_prob' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:3409:35: style: Variable 'middle_univdiagonal' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:3413:85: style: Unused variable: ninserts [unusedVariable]
gmap-2025-07-31/src/splice.c:3457:7: style: Unused variable: nmatches_trim_i [unusedVariable]
gmap-2025-07-31/src/splice.c:3457:24: style: Unused variable: nmatches_trim_j [unusedVariable]
gmap-2025-07-31/src/splice.c:3458:5: style: Unused variable: nmismatches_trim_i [unusedVariable]
gmap-2025-07-31/src/splice.c:3458:25: style: Unused variable: nmismatches_trim_j [unusedVariable]
gmap-2025-07-31/src/splice.c:3459:7: style: Unused variable: endpoint_i [unusedVariable]
gmap-2025-07-31/src/splice.c:3459:19: style: Unused variable: endpoint_j [unusedVariable]
gmap-2025-07-31/src/splice.c:4684:35: style: Variable 'middle_univdiagonal' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splice.c:4688:85: style: Unused variable: ninserts [unusedVariable]
gmap-2025-07-31/src/splice.c:4699:7: style: Unused variable: splice_region_low [unusedVariable]
gmap-2025-07-31/src/splice.c:4699:26: style: Unused variable: splice_region_high [unusedVariable]
gmap-2025-07-31/src/splice.c:4732:7: style: Unused variable: nmatches_trim_i [unusedVariable]
gmap-2025-07-31/src/splice.c:4732:24: style: Unused variable: nmatches_trim_j [unusedVariable]
gmap-2025-07-31/src/splice.c:4733:5: style: Unused variable: nmismatches_trim_i [unusedVariable]
gmap-2025-07-31/src/splice.c:4733:25: style: Unused variable: nmismatches_trim_j [unusedVariable]
gmap-2025-07-31/src/splice.c:4734:7: style: Unused variable: endpoint_i [unusedVariable]
gmap-2025-07-31/src/splice.c:4734:19: style: Unused variable: endpoint_j [unusedVariable]
gmap-2025-07-31/src/splice.c:6359:17: style: Variable 'invertedp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splicetrie.c:206:48: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:304:43: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:391:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:393:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:393:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:393:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:394:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:394:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:394:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:394:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:395:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:398:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:404:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:406:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:406:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:406:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:407:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:407:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:407:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:407:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:408:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:411:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:417:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:419:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:419:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:419:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:420:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:420:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:420:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:420:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:421:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:424:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:430:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:432:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:432:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:432:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:433:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:433:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:433:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:433:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:434:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:437:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:493:48: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:588:43: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:672:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:674:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:674:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:674:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:675:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:675:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:675:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:675:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:676:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:679:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:685:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:687:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:687:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:687:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:688:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:688:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:688:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:688:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:689:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:692:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:698:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:700:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:700:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:700:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:701:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:701:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:701:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:701:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:702:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:705:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:711:35: style: Redundant pointer operation on 'coordsptr' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:713:7: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:713:22: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:713:35: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:714:7: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:714:18: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:714:30: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:714:47: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:715:7: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:718:25: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:765:5: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:765:20: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:765:33: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:766:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:766:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:766:28: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:766:45: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:767:5: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:770:23: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:832:5: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:832:20: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:832:33: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:833:5: style: Redundant pointer operation on 'nopens' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:833:16: style: Redundant pointer operation on 'nindels' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:833:28: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:833:45: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:834:5: style: Redundant pointer operation on 'threshold_miss_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:837:23: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/splicetrie.c:238:27: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splicetrie.c:275:31: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splicetrie.c:523:27: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/splicetrie.c:559:31: style: Variable 'shortest_intron_length' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1.c:2781:48: style:inconclusive: Boolean expression 'heap[3]->diagonal==heap[2]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2025-07-31/src/stage1.c:2792:60: style:inconclusive: Boolean expression 'heap[righti]->diagonal==heap[smallesti]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2025-07-31/src/stage1.c:2873:50: style:inconclusive: Boolean expression 'heap[3]->diagonal==heap[2]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2025-07-31/src/stage1.c:2888:62: style:inconclusive: Boolean expression 'heap[righti]->diagonal==heap[smallesti]->diagonal' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
gmap-2025-07-31/src/stage1.c:3954:13: style: Variable 'trimstart' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1.c:3899:13: note: trimstart is assigned
gmap-2025-07-31/src/stage1.c:3954:13: note: trimstart is overwritten
gmap-2025-07-31/src/stage1.c:3955:11: style: Variable 'trimend' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1.c:3900:11: note: trimend is assigned
gmap-2025-07-31/src/stage1.c:3955:11: note: trimend is overwritten
gmap-2025-07-31/src/stage1.c:4090:16: style: Variable 'maxexons' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1.c:4047:16: note: maxexons is assigned
gmap-2025-07-31/src/stage1.c:4090:16: note: maxexons is overwritten
gmap-2025-07-31/src/stage1.c:1132:29: style: Redundant pointer operation on 'nnew' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:1132:38: style: Redundant pointer operation on 'overflowp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:1141:29: style: Redundant pointer operation on 'nnew' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:1141:38: style: Redundant pointer operation on 'overflowp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:1152:29: style: Redundant pointer operation on 'nnew' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:1152:38: style: Redundant pointer operation on 'overflowp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:1983:26: style: Redundant pointer operation on 'foundpairp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:2031:26: style: Redundant pointer operation on 'foundpairp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1.c:631:35: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:704:50: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:908:35: style: Parameter 'positions0' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:909:18: style: Parameter 'positions1' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:909:60: style: Parameter 'positions2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:1091:8: style: Variable 'npositions' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage1.c:1664:36: style: Parameter 'npositions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:2547:51: style: Parameter 'ndiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:2694:62: style: Parameter 'ndiagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:2930:21: style: Variable 'segmentj' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage1.c:3311:55: style: Parameter 'prev' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:3311:66: style: Parameter 'scores' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1.c:1759:8: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1.c:1765:12: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1.c:1800:8: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1.c:1806:12: style: Variable 'lastj' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1.c:2600:33: style: Variable 'last_diagonal' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-single.c:199:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage1hr-single.c:267:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage1hr-single.c:251:25: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:252:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:252:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:253:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:253:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:342:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:364:25: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:378:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:400:25: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:414:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:435:25: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:449:15: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:469:25: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:504:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:516:53: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:533:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:545:53: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:562:56: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:574:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:591:56: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:603:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:639:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:640:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:640:32: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:655:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:656:7: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:656:33: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:750:45: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:779:45: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:804:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:806:9: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:806:31: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:807:9: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:807:35: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:827:49: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:842:23: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:844:9: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:844:31: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:845:9: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:845:35: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:863:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:864:5: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:864:27: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:879:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:880:5: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:880:27: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:896:30: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:897:9: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:897:35: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:912:30: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:913:9: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:913:35: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1045:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1047:7: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1047:29: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1077:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1079:7: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1079:30: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1144:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1146:10: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1146:43: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1147:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1147:32: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1174:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1176:10: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1176:44: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1177:10: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1177:33: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1237:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1239:10: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1239:43: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1240:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1240:32: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1268:31: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1270:10: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1270:44: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1271:10: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1271:33: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1389:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1391:10: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1391:32: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1392:10: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1392:36: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1394:10: style: Redundant pointer operation on 'unextended_sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1394:43: style: Redundant pointer operation on 'unextended_sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1395:10: style: Redundant pointer operation on 'unextended_antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1395:47: style: Redundant pointer operation on 'unextended_antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1622:36: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1622:55: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1623:8: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1623:24: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-single.c:1593:7: warning: Uninitialized variables: paths.first, paths.rest [uninitvar]
gmap-2025-07-31/src/stage1hr-single.c:1510:74: note: Assuming condition is false
gmap-2025-07-31/src/stage1hr-single.c:1593:7: note: Uninitialized variables: paths.first, paths.rest
gmap-2025-07-31/src/stage1hr-single.c:1031:24: style: Variable 'any_imperfect_ends_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-single.c:1060:23: style: Variable 'any_imperfect_ends_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-single.c:1092:23: style: Variable 'any_imperfect_ends_p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-single.c:1437:8: style: Unused variable: any_imperfect_ends_p [unusedVariable]
gmap-2025-07-31/src/stage1hr.c:1839:35: style: Redundant pointer operation on 'sense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr.c:1839:57: style: Redundant pointer operation on 'antisense_paths_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr.c:1841:35: style: Redundant pointer operation on 'sense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr.c:1841:58: style: Redundant pointer operation on 'antisense_paths_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1117:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage1hr-paired.c:2327:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage1hr-paired.c:4092:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage1hr-paired.c:6920:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage1hr.c:669:41: style: Variable 'query_lastpos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage2.c:5746:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage2.c:5778:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage2.c:5810:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage2.c:5842:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage2.c:5930:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable genomepos [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:2279:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:2612:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:5637:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:5770:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:6415:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:10692:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gapp [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:11807:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stage3.c:12344:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gapp [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/spliceends.c:5113:16: style: The comparison 'donep == 0' is always true. [knownConditionTrueFalse]
gmap-2025-07-31/src/spliceends.c:5080:16: note: 'donep' is assigned value '0' here.
gmap-2025-07-31/src/spliceends.c:5113:16: note: The comparison 'donep == 0' is always true.
gmap-2025-07-31/src/spliceends.c:5554:16: style: The comparison 'donep == 0' is always true. [knownConditionTrueFalse]
gmap-2025-07-31/src/spliceends.c:5520:16: note: 'donep' is assigned value '0' here.
gmap-2025-07-31/src/spliceends.c:5554:16: note: The comparison 'donep == 0' is always true.
gmap-2025-07-31/src/spliceends.c:5105:11: style: Redundant initialization for 'trimpos'. The initialized value is overwritten before it is read. [redundantInitialization]
gmap-2025-07-31/src/spliceends.c:5079:15: note: trimpos is initialized
gmap-2025-07-31/src/spliceends.c:5105:11: note: trimpos is overwritten
gmap-2025-07-31/src/spliceends.c:5546:11: style: Redundant initialization for 'trimpos'. The initialized value is overwritten before it is read. [redundantInitialization]
gmap-2025-07-31/src/spliceends.c:5519:15: note: trimpos is initialized
gmap-2025-07-31/src/spliceends.c:5546:11: note: trimpos is overwritten
gmap-2025-07-31/src/spliceends.c:1686:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1687:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1739:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1740:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1776:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1777:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1793:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1794:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1904:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1905:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1958:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1959:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1995:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:1996:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2012:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2013:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2296:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2297:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2349:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2350:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2386:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2387:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2403:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2404:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2515:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2516:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2568:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2569:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2605:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2606:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2622:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2623:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2862:58: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:2875:61: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3804:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3805:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3857:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3858:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3894:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3895:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3911:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:3912:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4024:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4025:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4077:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4078:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4114:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4115:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4131:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4132:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4418:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4419:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4471:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4472:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4508:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4509:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4525:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4526:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4638:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4639:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4691:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4692:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4728:42: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4729:11: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4745:43: style: Redundant pointer operation on 'max_prob' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4746:5: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:4989:58: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5002:61: style: Redundant pointer operation on 'partnerp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5283:48: style: Redundant pointer operation on 'nosplice_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5339:37: style: Redundant pointer operation on 'new' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5396:39: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5721:46: style: Redundant pointer operation on 'nosplice_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5777:37: style: Redundant pointer operation on 'new' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5833:37: style: Redundant pointer operation on 'nmismatches_to_trimpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5987:73: style: Redundant pointer operation on 'local_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:6061:73: style: Redundant pointer operation on 'local_nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/spliceends.c:5247:60: style:inconclusive: Function 'Spliceends_trimmed_qstarts' argument 25 names different: declaration 'localdb_all' definition 'localdb_alloc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/spliceends.h:119:60: note: Function 'Spliceends_trimmed_qstarts' argument 25 names different: declaration 'localdb_all' definition 'localdb_alloc'.
gmap-2025-07-31/src/spliceends.c:5247:60: note: Function 'Spliceends_trimmed_qstarts' argument 25 names different: declaration 'localdb_all' definition 'localdb_alloc'.
gmap-2025-07-31/src/spliceends.c:537:21: style: Parameter 'splice_qpos' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:551:21: style: Parameter 'splice_qpos' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:594:16: style: Variable 'positions' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:972:29: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:983:38: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:994:51: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:1125:73: style: Parameter 'sitep' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:1529:9: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:1541:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:1541:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:2140:15: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:2152:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:2152:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:2952:16: style: Variable 'positions' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:3244:73: style: Parameter 'sitep' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:3644:9: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:3657:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:3657:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:4259:15: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:4272:16: style: Variable 'endpoints_inward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:4272:35: style: Variable 'endpoints_outward' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/spliceends.c:5076:68: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:5516:66: style: Parameter 'mismatch_positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/spliceends.c:5649:19: style: Variable 'nunivdiags' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stopwatch.c:76:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCK_MONOTONIC [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/stopwatch.c:107:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCK_MONOTONIC [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/support.c:665:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/support.c:754:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/support.c:932:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/support.c:706:7: warning: %u in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
gmap-2025-07-31/src/support.c:713:7: warning: %u in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
gmap-2025-07-31/src/support.c:720:7: warning: %u in format string (no. 1) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
gmap-2025-07-31/src/support.c:477:10: style: Variable 'chrnum' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/support.c:432:10: note: chrnum is assigned
gmap-2025-07-31/src/support.c:477:10: note: chrnum is overwritten
gmap-2025-07-31/src/support.c:477:10: style: Variable 'chrnum' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/support.c:453:9: note: chrnum is assigned
gmap-2025-07-31/src/support.c:477:10: note: chrnum is overwritten
gmap-2025-07-31/src/support.c:664:23: style: Redundant pointer operation on 'low_chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/support.c:671:23: style: Redundant pointer operation on 'high_chrpos' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/support.c:622:19: style: Parameter 'last_chr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/support.c:623:20: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/support.c:640:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/support.c:812:3: warning: Uninitialized variable: last_chr [uninitvar]
gmap-2025-07-31/src/support.c:751:15: note: Assuming condition is false
gmap-2025-07-31/src/support.c:812:3: note: Uninitialized variable: last_chr
gmap-2025-07-31/src/support.c:477:10: style: Variable 'chrnum' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/support.c:498:9: style: Variable 'chrnum' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/support.c:724:7: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/table.c:65:35: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2025-07-31/src/table.c:78:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/table.c:42:9: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/table.c:43:9: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/table.c:68:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/table.c:242:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/table.c:243:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/table.c:167:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/tableint.c:43:38: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2025-07-31/src/tableint.c:56:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/tableint.c:46:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/tableint.c:181:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableint.c:182:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableint.c:223:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableint.c:224:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableint.c:266:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableint.c:131:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/tableuint.c:44:39: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2025-07-31/src/tableuint.c:57:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/tableuint.c:47:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/tableuint.c:182:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableuint.c:183:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableuint.c:232:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableuint.c:132:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/tableuint8.c:44:39: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
gmap-2025-07-31/src/tableuint8.c:57:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/tableuint8.c:241:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/tableuint8.c:47:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/tableuint8.c:195:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableuint8.c:196:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableuint8.c:238:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/tableuint8.c:145:9: style: Variable 'stamp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage2.c:1558:24: style: Condition 'processed==NULL' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage2.c:2490:24: style: Condition 'processed==NULL' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage2.c:657:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/stage2.c:669:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/stage2.c:1138:43: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage2.c:1137:18: note: prevposition is assigned
gmap-2025-07-31/src/stage2.c:1138:43: note: prevposition is overwritten
gmap-2025-07-31/src/stage2.c:1690:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage2.c:1689:20: note: prevposition is assigned
gmap-2025-07-31/src/stage2.c:1690:45: note: prevposition is overwritten
gmap-2025-07-31/src/stage2.c:1714:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage2.c:1713:20: note: prevposition is assigned
gmap-2025-07-31/src/stage2.c:1714:45: note: prevposition is overwritten
gmap-2025-07-31/src/stage2.c:2083:43: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage2.c:2082:18: note: prevposition is assigned
gmap-2025-07-31/src/stage2.c:2083:43: note: prevposition is overwritten
gmap-2025-07-31/src/stage2.c:2624:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage2.c:2623:20: note: prevposition is assigned
gmap-2025-07-31/src/stage2.c:2624:45: note: prevposition is overwritten
gmap-2025-07-31/src/stage2.c:2648:45: style: Variable 'prevposition' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage2.c:2647:20: note: prevposition is assigned
gmap-2025-07-31/src/stage2.c:2648:45: note: prevposition is overwritten
gmap-2025-07-31/src/stage2.c:4107:25: style: Redundant pointer operation on 'ncells' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage2.c:4128:28: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage2.c:5049:25: style: Redundant pointer operation on 'ncells' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage2.c:402:38: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:428:38: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:644:33: style: Parameter 'minactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:644:54: style: Parameter 'maxactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:1075:28: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:1085:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:1086:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:1470:24: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:1472:50: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:1486:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:1486:29: style: Variable 'adj_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:1487:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:1487:22: style: Variable 'adj_active' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:2022:45: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:2033:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:2034:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:2404:20: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:2406:46: style: Parameter 'firstactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:2420:13: style: Variable 'prev_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:2420:29: style: Variable 'adj_mappings' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:2421:8: style: Variable 'prev_active' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:2421:22: style: Variable 'adj_active' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage2.c:3111:37: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:3136:37: style: Parameter 'lengths2' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:3437:44: style: Parameter 'npositions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:3668:41: style: Parameter 'minactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:3668:62: style: Parameter 'maxactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:4140:15: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:4140:35: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:4314:13: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:4611:37: style: Parameter 'minactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:4611:58: style: Parameter 'maxactive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:5335:10: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:5335:30: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage2.c:5733:10: warning: Uninitialized variable: ncovered [uninitvar]
gmap-2025-07-31/src/stage2.c:5653:57: note: Assuming condition is false
gmap-2025-07-31/src/stage2.c:5733:10: note: Uninitialized variable: ncovered
gmap-2025-07-31/src/stage2.c:6509:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2025-07-31/src/stage2.c:6461:57: note: Assuming condition is false
gmap-2025-07-31/src/stage2.c:6509:18: note: Uninitialized variable: indexsize
gmap-2025-07-31/src/stage2.c:6843:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2025-07-31/src/stage2.c:6797:57: note: Assuming condition is false
gmap-2025-07-31/src/stage2.c:6843:18: note: Uninitialized variable: indexsize
gmap-2025-07-31/src/stage2.c:7004:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2025-07-31/src/stage2.c:6958:57: note: Assuming condition is false
gmap-2025-07-31/src/stage2.c:7004:18: note: Uninitialized variable: indexsize
gmap-2025-07-31/src/stage2.c:7178:18: warning: Uninitialized variable: indexsize [uninitvar]
gmap-2025-07-31/src/stage2.c:7131:57: note: Assuming condition is false
gmap-2025-07-31/src/stage2.c:7178:18: note: Uninitialized variable: indexsize
gmap-2025-07-31/src/stage2.c:4165:16: style: Variable 'position' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6733:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1hr-paired.c:6725:10: note: lowp is assigned
gmap-2025-07-31/src/stage1hr-paired.c:6733:10: note: lowp is overwritten
gmap-2025-07-31/src/stage1hr-paired.c:6751:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1hr-paired.c:6744:10: note: lowp is assigned
gmap-2025-07-31/src/stage1hr-paired.c:6751:10: note: lowp is overwritten
gmap-2025-07-31/src/stage1hr-paired.c:6768:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1hr-paired.c:6761:10: note: lowp is assigned
gmap-2025-07-31/src/stage1hr-paired.c:6768:10: note: lowp is overwritten
gmap-2025-07-31/src/stage1hr-paired.c:6789:10: style: Variable 'lowp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1hr-paired.c:6781:10: note: lowp is assigned
gmap-2025-07-31/src/stage1hr-paired.c:6789:10: note: lowp is overwritten
gmap-2025-07-31/src/stage1hr-paired.c:6961:5: style: Variable 'found_score_5' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2025-07-31/src/stage1hr-paired.c:6874:17: note: found_score_5 is assigned 'querylength5' here.
gmap-2025-07-31/src/stage1hr-paired.c:6961:5: note: Variable 'found_score_5' is assigned an expression that holds the same value.
gmap-2025-07-31/src/stage1hr-paired.c:6962:5: style: Variable 'found_score_3' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2025-07-31/src/stage1hr-paired.c:6875:17: note: found_score_3 is assigned 'querylength3' here.
gmap-2025-07-31/src/stage1hr-paired.c:6962:5: note: Variable 'found_score_3' is assigned an expression that holds the same value.
gmap-2025-07-31/src/stage1hr-paired.c:7314:18: style: Variable 'solved_all_p' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage1hr-paired.c:7249:18: note: solved_all_p is assigned
gmap-2025-07-31/src/stage1hr-paired.c:7314:18: note: solved_all_p is overwritten
gmap-2025-07-31/src/stage1hr-paired.c:6923:5: style:inconclusive: Statements following noreturn function 'exit()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/stage1hr-paired.c:344:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:370:49: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:408:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:434:49: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:453:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:453:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:453:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:474:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:474:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:474:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:520:46: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:555:51: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:591:46: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:626:51: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:662:46: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:697:51: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:733:46: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:768:51: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:825:47: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:838:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:838:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:838:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:861:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:861:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:861:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:915:47: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:928:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:928:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:928:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:951:30: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:951:53: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:951:71: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1015:19: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1047:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1085:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1226:29: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1272:29: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1576:34: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1576:57: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1805:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1805:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1830:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1830:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1847:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1847:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1886:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1886:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1911:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1911:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1928:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:1928:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2057:8: style: Redundant pointer operation on 'found_score_L' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2134:8: style: Redundant pointer operation on 'found_score_H' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2201:26: style: Redundant pointer operation on 'completeL_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2201:42: style: Redundant pointer operation on 'completeH_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2201:58: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2202:6: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2213:27: style: Redundant pointer operation on 'completeL_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2213:43: style: Redundant pointer operation on 'completeH_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2213:59: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2214:6: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2257:25: style: Redundant pointer operation on 'querystart' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2257:40: style: Redundant pointer operation on 'queryend' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2258:17: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2258:42: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2259:3: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2259:24: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2260:3: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2260:29: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2261:3: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2261:25: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2275:22: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2275:47: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2276:8: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2276:29: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2277:8: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2277:34: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2278:8: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2278:30: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2296:18: style: Redundant pointer operation on '_univdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2296:43: style: Redundant pointer operation on 'auxinfo_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2297:4: style: Redundant pointer operation on 'pathstores_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2297:25: style: Redundant pointer operation on 'nunivdiagonals_gplus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2298:4: style: Redundant pointer operation on '_univdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2298:30: style: Redundant pointer operation on 'auxinfo_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2299:4: style: Redundant pointer operation on 'pathstores_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2299:26: style: Redundant pointer operation on 'nunivdiagonals_gminus' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2679:35: style: Redundant pointer operation on 'last_method_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2691:35: style: Redundant pointer operation on 'last_method_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2789:43: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2789:59: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2790:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2790:31: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2790:49: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2791:8: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2818:43: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2818:59: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2819:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2819:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2819:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2820:8: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2848:43: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2848:59: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2848:75: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2849:8: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2849:26: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2850:8: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2878:43: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2878:59: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2879:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2879:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2879:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2880:8: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2908:43: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2908:59: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2909:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2909:31: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2909:49: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2910:8: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2938:43: style: Redundant pointer operation on 'complete3_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2938:59: style: Redundant pointer operation on 'complete5_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2939:8: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2939:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2939:49: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:2940:8: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3210:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3227:28: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3599:48: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3599:71: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3599:89: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3638:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3638:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3638:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3662:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3662:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3662:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3686:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3686:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3686:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3710:53: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3710:76: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3710:94: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3741:40: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:3754:40: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4123:46: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4170:46: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4217:38: style: Redundant pointer operation on 'npaths5_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4217:58: style: Redundant pointer operation on 'npaths5_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4217:77: style: Redundant pointer operation on 'first_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4217:94: style: Redundant pointer operation on 'second_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4234:38: style: Redundant pointer operation on 'npaths3_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4234:58: style: Redundant pointer operation on 'npaths3_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4234:77: style: Redundant pointer operation on 'first_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4234:94: style: Redundant pointer operation on 'second_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4314:44: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4314:62: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4315:9: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4315:28: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4315:46: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4315:62: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4549:31: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4589:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4614:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4614:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4658:31: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4698:31: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4723:29: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:4723:52: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5022:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5045:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5045:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5118:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5141:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5141:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5228:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5251:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5251:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5324:33: style: Redundant pointer operation on 'found_score_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5347:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5347:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5560:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5583:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5583:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5656:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5679:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5679:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5767:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5790:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5790:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5863:33: style: Redundant pointer operation on 'found_score_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5886:31: style: Redundant pointer operation on 'found_score_paired' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:5886:54: style: Redundant pointer operation on 'unresolved_pathpairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:6678:11: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:6704:11: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7440:9: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7440:28: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7440:46: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7440:62: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7523:57: style: Redundant pointer operation on 'final_pairtype' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7524:6: style: Redundant pointer operation on 'npaths_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7524:25: style: Redundant pointer operation on 'npaths_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7524:43: style: Redundant pointer operation on 'first_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7524:59: style: Redundant pointer operation on 'second_absmq' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7525:6: style: Redundant pointer operation on 'patharray5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7525:21: style: Redundant pointer operation on 'npaths5_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7525:41: style: Redundant pointer operation on 'npaths5_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7525:60: style: Redundant pointer operation on 'first_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7525:77: style: Redundant pointer operation on 'second_absmq5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7526:6: style: Redundant pointer operation on 'patharray3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7526:21: style: Redundant pointer operation on 'npaths3_primary' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7526:41: style: Redundant pointer operation on 'npaths3_altloc' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7526:60: style: Redundant pointer operation on 'first_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:7526:77: style: Redundant pointer operation on 'second_absmq3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage1hr-paired.c:6805:33: style:inconclusive: Function 'Stage1_paired_read' argument 7 names different: declaration 'nhits5_primary' definition 'npaths5_primary'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage1hr-paired.h:36:33: note: Function 'Stage1_paired_read' argument 7 names different: declaration 'nhits5_primary' definition 'npaths5_primary'.
gmap-2025-07-31/src/stage1hr-paired.c:6805:33: note: Function 'Stage1_paired_read' argument 7 names different: declaration 'nhits5_primary' definition 'npaths5_primary'.
gmap-2025-07-31/src/stage1hr-paired.c:6805:55: style:inconclusive: Function 'Stage1_paired_read' argument 8 names different: declaration 'nhits5_altloc' definition 'npaths5_altloc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage1hr-paired.h:36:54: note: Function 'Stage1_paired_read' argument 8 names different: declaration 'nhits5_altloc' definition 'npaths5_altloc'.
gmap-2025-07-31/src/stage1hr-paired.c:6805:55: note: Function 'Stage1_paired_read' argument 8 names different: declaration 'nhits5_altloc' definition 'npaths5_altloc'.
gmap-2025-07-31/src/stage1hr-paired.c:6806:33: style:inconclusive: Function 'Stage1_paired_read' argument 12 names different: declaration 'nhits3_primary' definition 'npaths3_primary'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage1hr-paired.h:37:33: note: Function 'Stage1_paired_read' argument 12 names different: declaration 'nhits3_primary' definition 'npaths3_primary'.
gmap-2025-07-31/src/stage1hr-paired.c:6806:33: note: Function 'Stage1_paired_read' argument 12 names different: declaration 'nhits3_primary' definition 'npaths3_primary'.
gmap-2025-07-31/src/stage1hr-paired.c:6806:55: style:inconclusive: Function 'Stage1_paired_read' argument 13 names different: declaration 'nhits3_altloc' definition 'npaths3_altloc'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage1hr-paired.h:37:54: note: Function 'Stage1_paired_read' argument 13 names different: declaration 'nhits3_altloc' definition 'npaths3_altloc'.
gmap-2025-07-31/src/stage1hr-paired.c:6806:55: note: Function 'Stage1_paired_read' argument 13 names different: declaration 'nhits3_altloc' definition 'npaths3_altloc'.
gmap-2025-07-31/src/stage1hr-paired.c:7573:62: style:inconclusive: Function 'Stage1hr_paired_setup' argument 14 names different: declaration 'shortsplicedist_in' definition 'shortsplicedist'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage1hr-paired.h:58:62: note: Function 'Stage1hr_paired_setup' argument 14 names different: declaration 'shortsplicedist_in' definition 'shortsplicedist'.
gmap-2025-07-31/src/stage1hr-paired.c:7573:62: note: Function 'Stage1hr_paired_setup' argument 14 names different: declaration 'shortsplicedist_in' definition 'shortsplicedist'.
gmap-2025-07-31/src/stage1hr-paired.c:1355:32: style: Parameter 'completeL_p' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:1355:51: style: Parameter 'completeH_p' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:1358:10: style: Parameter 'indices' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:1593:33: style: Parameter 'completeL_p' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:1593:52: style: Parameter 'completeH_p' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:1596:11: style: Parameter 'indices' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:4749:51: style: Parameter 'exhaustive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:4749:68: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:4766:53: style: Parameter 'exhaustive' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:4766:70: style: Parameter 'counts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage1hr-paired.c:4377:10: 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-2025-07-31/src/stage1hr-paired.c:4303:17: note: Assuming condition is false
gmap-2025-07-31/src/stage1hr-paired.c:4342:44: note: Assuming condition is true
gmap-2025-07-31/src/stage1hr-paired.c:4377:10: 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-2025-07-31/src/stage1hr-paired.c:1611:15: style: Unused variable: univdiagonalL [unusedVariable]
gmap-2025-07-31/src/stage1hr-paired.c:1611:30: style: Unused variable: univdiagonalH [unusedVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6733:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6751:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6768:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6789:10: style: Variable 'lowp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6842:26: style: Variable 'max_nintersections' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6822:28: style: Variable 'unextended_pathpairs' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6842:7: style: Variable 'max_nintersections' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6854:8: style: Unused variable: mismatch_positions_alloc_5 [unusedVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6854:37: style: Unused variable: mismatch_positions_alloc_3 [unusedVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6855:15: style: Unused variable: univdiagonal_L [unusedVariable]
gmap-2025-07-31/src/stage1hr-paired.c:6855:31: style: Unused variable: univdiagonal_H [unusedVariable]
gmap-2025-07-31/src/tr-extension-search.c:664:35: style: Condition '(queryoffset=plus_qpos)>=query_lastpos' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/tr-extension-search.c:663:13: note: Assuming that condition 'plus_qpos<query_lastpos' is not redundant
gmap-2025-07-31/src/tr-extension-search.c:664:35: note: Condition '(queryoffset=plus_qpos)>=query_lastpos' is always false
gmap-2025-07-31/src/tr-extension-search.c:709:36: style: Condition '(queryoffset=minus_qpos)>=query_lastpos' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/tr-extension-search.c:663:43: note: Assuming that condition 'minus_qpos<query_lastpos' is not redundant
gmap-2025-07-31/src/tr-extension-search.c:709:36: note: Condition '(queryoffset=minus_qpos)>=query_lastpos' is always false
gmap-2025-07-31/src/tr-extension-search.c:914:35: style: Condition '(queryoffset=plus_qpos)<0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/tr-extension-search.c:913:13: note: Assuming that condition 'plus_qpos>0' is not redundant
gmap-2025-07-31/src/tr-extension-search.c:914:35: note: Condition '(queryoffset=plus_qpos)<0' is always false
gmap-2025-07-31/src/tr-extension-search.c:959:36: style: Condition '(queryoffset=minus_qpos)<0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/tr-extension-search.c:913:31: note: Assuming that condition 'minus_qpos>0' is not redundant
gmap-2025-07-31/src/tr-extension-search.c:959:36: note: Condition '(queryoffset=minus_qpos)<0' is always false
gmap-2025-07-31/src/tr-extension-search.c:172:22: style: Redundant pointer operation on 'set' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:824:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:834:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:851:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:853:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1077:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1087:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1104:24: style: Redundant pointer operation on 'best_plus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1106:24: style: Redundant pointer operation on 'best_minus_elts' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1373:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1393:47: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1618:18: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1619:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1619:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1620:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1620:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1731:18: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1732:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1732:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1733:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1733:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1844:18: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1845:4: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1845:30: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1846:4: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1846:22: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1905:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1906:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1906:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1907:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1907:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1916:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1917:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1917:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1918:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1918:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1927:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1928:10: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1928:36: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1929:10: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1929:28: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1943:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1944:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1944:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1945:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1945:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1954:27: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1955:6: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1955:32: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1956:6: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1956:24: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1965:24: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1966:10: style: Redundant pointer operation on 'partial_sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1966:36: style: Redundant pointer operation on 'partial_antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1967:10: style: Redundant pointer operation on 'sense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:1967:28: style: Redundant pointer operation on 'antisense_trpaths' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/tr-extension-search.c:250:27: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/tr-extension-search.c:363:27: style: Parameter 'positions' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:935:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
gmap-2025-07-31/src/transcript-remap.c:67:35: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:67:57: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:77:56: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:111:36: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:111:58: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:121:57: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:1206:11: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:1206:33: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:1232:12: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-remap.c:1232:34: style: Parameter 'exonstarts' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcript-velocity.c:273:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/transcript-velocity.c:347:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/transcript-remap.c:935:10: style: Variable 'path' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/transcript.c:859:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/transcript.c:1078:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/transcript.c:616:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2025-07-31/src/transcript.c:615:25: note: outer condition: q!=NULL
gmap-2025-07-31/src/transcript.c:616:11: note: opposite inner condition: q==NULL
gmap-2025-07-31/src/transcript.c:654:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2025-07-31/src/transcript.c:653:25: note: outer condition: r!=NULL
gmap-2025-07-31/src/transcript.c:654:11: note: opposite inner condition: r==NULL
gmap-2025-07-31/src/transcript.c:693:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2025-07-31/src/transcript.c:692:25: note: outer condition: q!=NULL
gmap-2025-07-31/src/transcript.c:693:11: note: opposite inner condition: q==NULL
gmap-2025-07-31/src/transcript.c:732:11: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
gmap-2025-07-31/src/transcript.c:731:25: note: outer condition: r!=NULL
gmap-2025-07-31/src/transcript.c:732:11: note: opposite inner condition: r==NULL
gmap-2025-07-31/src/transcript.c:70:34: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcript.c:87:22: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/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-2025-07-31/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-2025-07-31/src/transcriptome.c:133:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/transcriptome.c:104:26: style: Parameter 'genomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcriptome.c:104:46: style: Parameter 'genome_fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcriptome.c:105:12: style: Parameter 'transcriptomesubdir' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcriptome.c:105:39: style: Parameter 'transcriptome_fileroot' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:315:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/translation.c:455:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/translation.c:703:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/translation.c:778:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/transcriptome-search.c:436:43: style: Redundant pointer operation on 'n_sense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:440:47: style: Redundant pointer operation on 'n_antisense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:1330:26: style: Redundant pointer operation on 'ndiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:1350:26: style: Redundant pointer operation on 'ndiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:1394:43: style: Redundant pointer operation on 'n_sense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:1401:47: style: Redundant pointer operation on 'n_antisense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:1408:43: style: Redundant pointer operation on 'n_sense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:1411:47: style: Redundant pointer operation on 'n_antisense_trdiagonals' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/transcriptome-search.c:393:14: style: Variable 'tplus_positions_end5' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/transcriptome-search.c:393:44: style: Variable 'tminus_positions_end5' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/transcriptome-search.c:394:6: style: Variable 'tplus_positions_end3' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/transcriptome-search.c:394:36: style: Variable 'tminus_positions_end3' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/transcriptome-search.c:1241:28: style: Parameter 'diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcriptome-search.c:1264:46: style: Parameter 'all_diagonals' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/transcriptome-search.c:395:30: style: Variable 'n_tplus_positions_end5' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/transcriptome-search.c:395:59: style: Variable 'n_tminus_positions_end5' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/transcriptome-search.c:396:28: style: Variable 'n_tplus_positions_end3' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/transcriptome-search.c:396:57: style: Variable 'n_tminus_positions_end3' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trindex.c:191:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/trindex.c:429:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/trindex.c:365:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/trindex.c:326:13: note: Assuming allocation function fails
gmap-2025-07-31/src/trindex.c:326:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2025-07-31/src/trindex.c:365:10: note: Null pointer dereference
gmap-2025-07-31/src/trindex.c:372:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/trindex.c:369:13: note: Assuming allocation function fails
gmap-2025-07-31/src/trindex.c:369:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2025-07-31/src/trindex.c:372:3: note: Null pointer dereference
gmap-2025-07-31/src/trindex.c:373:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/trindex.c:369:13: note: Assuming allocation function fails
gmap-2025-07-31/src/trindex.c:369:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2025-07-31/src/trindex.c:373:10: note: Null pointer dereference
gmap-2025-07-31/src/trindex.c:383:3: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/trindex.c:380:13: note: Assuming allocation function fails
gmap-2025-07-31/src/trindex.c:380:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2025-07-31/src/trindex.c:383:3: note: Null pointer dereference
gmap-2025-07-31/src/trindex.c:384:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
gmap-2025-07-31/src/trindex.c:380:13: note: Assuming allocation function fails
gmap-2025-07-31/src/trindex.c:380:13: note: Assignment 'fp=fopen(filename,"wb")', assigned value is 0
gmap-2025-07-31/src/trindex.c:384:10: note: Null pointer dereference
gmap-2025-07-31/src/trpath-eval.c:276:33: style:inconclusive: Function 'Trpath_eval_setup' argument 1 names different: declaration 'transcriptome_in' definition 'transcriptomebits_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/trpath-eval.h:26:33: note: Function 'Trpath_eval_setup' argument 1 names different: declaration 'transcriptome_in' definition 'transcriptomebits_in'.
gmap-2025-07-31/src/trpath-eval.c:276:33: note: Function 'Trpath_eval_setup' argument 1 names different: declaration 'transcriptome_in' definition 'transcriptomebits_in'.
gmap-2025-07-31/src/trpath-eval.c:262:38: warning: Uninitialized variable: qend [uninitvar]
gmap-2025-07-31/src/trpath-eval.c:212:91: note: Assuming condition is false
gmap-2025-07-31/src/trpath-eval.c:262:38: note: Uninitialized variable: qend
gmap-2025-07-31/src/trpath-eval.c:62:15: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-eval.c:205:15: style: Variable 'nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:532:7: style: Same expression used in consecutive assignments of 'start0' and 'start1'. [duplicateAssignExpression]
gmap-2025-07-31/src/translation.c:532:34: note: Same expression used in consecutive assignments of 'start0' and 'start1'.
gmap-2025-07-31/src/translation.c:532:7: note: Same expression used in consecutive assignments of 'start0' and 'start1'.
gmap-2025-07-31/src/translation.c:532:34: style: Same expression used in consecutive assignments of 'start1' and 'start2'. [duplicateAssignExpression]
gmap-2025-07-31/src/translation.c:532:61: note: Same expression used in consecutive assignments of 'start1' and 'start2'.
gmap-2025-07-31/src/translation.c:532:34: note: Same expression used in consecutive assignments of 'start1' and 'start2'.
gmap-2025-07-31/src/translation.c:1742:27: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/translation.c:1746:24: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/translation.c:1751:26: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/translation.c:1760:28: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/translation.c:1764:25: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/translation.c:1769:27: style: Redundant pointer operation on 'translation_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/translation.c:879:24: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:921:24: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:966:55: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:987:48: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:1007:53: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:1028:56: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:1048:49: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:1068:54: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:1427:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:1460:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:1511:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:1544:18: style: Variable 'pair' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:2236:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:2256:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:2279:84: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:2281:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:2326:62: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/translation.c:2328:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/translation.c:881:26: style: Variable 'nt2' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:923:26: style: Variable 'nt2' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:1442:10: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:1526:10: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:1996:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:2040:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:2082:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:2124:14: style: Variable 'refquerypos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:2447:16: style: Variable 'aapos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/translation.c:2470:16: style: Variable 'aapos' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-solve.c:110:11: style: Condition '0&&score>sufficient_score' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/trpath-solve.c:675:13: style: Condition '0&&score>sufficient_score' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/trpath-solve.c:555:32: warning: Either the condition 'tend_path!=NULL' is redundant or there is possible null pointer dereference: tend_trpath. [nullPointerRedundantCheck]
gmap-2025-07-31/src/trpath-solve.c:920:47: note: Assuming that condition 'tend_path!=NULL' is not redundant
gmap-2025-07-31/src/trpath-solve.c:922:62: note: Calling function 'combine_leftright_trpaths', 2nd argument 'tend_path' value is 0
gmap-2025-07-31/src/trpath-solve.c:555:32: note: Null pointer dereference
gmap-2025-07-31/src/trpath-solve.c:556:37: warning: Either the condition 'tend_path!=NULL' is redundant or there is possible null pointer dereference: tend_trpath. [nullPointerRedundantCheck]
gmap-2025-07-31/src/trpath-solve.c:920:47: note: Assuming that condition 'tend_path!=NULL' is not redundant
gmap-2025-07-31/src/trpath-solve.c:922:62: note: Calling function 'combine_leftright_trpaths', 2nd argument 'tend_path' value is 0
gmap-2025-07-31/src/trpath-solve.c:556:37: note: Null pointer dereference
gmap-2025-07-31/src/trpath-solve.c:127:17: style: Variable '*partialp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/trpath-solve.c:121:12: note: *partialp is assigned
gmap-2025-07-31/src/trpath-solve.c:127:17: note: *partialp is overwritten
gmap-2025-07-31/src/trpath-solve.c:127:17: style: Variable '*partialp' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/trpath-solve.c:123:12: note: *partialp is assigned
gmap-2025-07-31/src/trpath-solve.c:127:17: note: *partialp is overwritten
gmap-2025-07-31/src/trpath-solve.c:589:9: style: Variable 'tend1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/trpath-solve.c:552:9: note: tend1 is assigned
gmap-2025-07-31/src/trpath-solve.c:589:9: note: tend1 is overwritten
gmap-2025-07-31/src/trpath-solve.c:588:11: style: Variable 'tstart1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/trpath-solve.c:553:11: note: tstart1 is assigned
gmap-2025-07-31/src/trpath-solve.c:588:11: note: tstart1 is overwritten
gmap-2025-07-31/src/trpath-solve.c:593:11: style: Variable 'tstart2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/trpath-solve.c:555:11: note: tstart2 is assigned
gmap-2025-07-31/src/trpath-solve.c:593:11: note: tstart2 is overwritten
gmap-2025-07-31/src/trpath-solve.c:594:9: style: Variable 'tend2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/trpath-solve.c:556:9: note: tend2 is assigned
gmap-2025-07-31/src/trpath-solve.c:594:9: note: tend2 is overwritten
gmap-2025-07-31/src/trpath-solve.c:136:40: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-solve.c:136:56: style: Redundant pointer operation on 'partialp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-solve.c:953:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-solve.c:1196:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-solve.c:1205:60: style:inconclusive: Function 'Trpath_solve_setup' argument 6 names different: declaration 'index1part_tr' definition 'index1part_tr_in'. [funcArgNamesDifferent]
gmap-2025-07-31/src/trpath-solve.h:88:11: note: Function 'Trpath_solve_setup' argument 6 names different: declaration 'index1part_tr' definition 'index1part_tr_in'.
gmap-2025-07-31/src/trpath-solve.c:1205:60: note: Function 'Trpath_solve_setup' argument 6 names different: declaration 'index1part_tr' definition 'index1part_tr_in'.
gmap-2025-07-31/src/trpath-solve.c:819:22: style: Variable 'tstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-solve.c:895:20: style: Variable 'tend' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:689:41: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:753:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:1297:41: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:1360:26: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:1441:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:1475:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:1549:54: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:1582:55: style: Redundant pointer operation on 'found_score' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath-convert.c:59:42: style: Parameter 'exonbounds' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/trpath-convert.c:429:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:506:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:517:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:562:36: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:240:7: style: Unused variable: local_trimpos [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:240:22: style: Unused variable: local_nmismatches [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:241:7: style: Unused variable: ntrim_qstart [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:241:21: style: Unused variable: ntrim_qend [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:241:33: style: Unused variable: pos5 [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:241:39: style: Unused variable: pos3 [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:1036:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:1113:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:1124:25: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:1177:36: style: Variable 'trstart' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/trpath-convert.c:848:7: style: Unused variable: local_trimpos [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:848:22: style: Unused variable: local_nmismatches [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:849:7: style: Unused variable: ntrim_qstart [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:849:21: style: Unused variable: ntrim_qend [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:849:33: style: Unused variable: pos5 [unusedVariable]
gmap-2025-07-31/src/trpath-convert.c:849:39: style: Unused variable: pos3 [unusedVariable]
gmap-2025-07-31/src/uint8list.c:152:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/uint8list.c:170:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/uint8list.c:188:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/trpath.c:403:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'Trnum_T {aka unsigned int}'. [invalidPrintfArgType_sint]
gmap-2025-07-31/src/uint8list.c:269:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2025-07-31/src/uint8list.c:264:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2025-07-31/src/uint8list.c:266:20: note: Assuming condition is false
gmap-2025-07-31/src/uint8list.c:269:10: note: Null pointer dereference
gmap-2025-07-31/src/uint8list.c:91:23: style:inconclusive: Function 'Uint8list_head_set' argument 1 names different: declaration 'list' definition 'this'. [funcArgNamesDifferent]
gmap-2025-07-31/src/uint8list.h:110:23: note: Function 'Uint8list_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2025-07-31/src/uint8list.c:91:23: note: Function 'Uint8list_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2025-07-31/src/uint8list.c:225:30: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/trpath.c:109:26: style: Redundant pointer operation on 'old' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/trpath.c:127:25: style: Redundant pointer operation on 'list' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/uint8list.c:240:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2025-07-31/src/trpath.c:151:44: style:inconclusive: Function 'Trpath_new_for_tstart_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'. [funcArgNamesDifferent]
gmap-2025-07-31/src/trpath.h:78:44: note: Function 'Trpath_new_for_tstart_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2025-07-31/src/trpath.c:151:44: note: Function 'Trpath_new_for_tstart_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2025-07-31/src/trpath.c:191:42: style:inconclusive: Function 'Trpath_new_for_tend_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'. [funcArgNamesDifferent]
gmap-2025-07-31/src/trpath.h:85:42: note: Function 'Trpath_new_for_tend_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2025-07-31/src/trpath.c:191:42: note: Function 'Trpath_new_for_tend_extension' argument 1 names different: declaration 'univdiagonal' definition 'trdiagonal'.
gmap-2025-07-31/src/trpath.c:53:13: style: Unused variable: q [unusedVariable]
gmap-2025-07-31/src/trpath.c:327:13: style: Unused variable: q [unusedVariable]
gmap-2025-07-31/src/uint8tableuint.c:168:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/uint8tableuint.c:214:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT8 [valueFlowBailoutIncompleteVar]
gmap-2025-07-31/src/uint8tableuint.c:36:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/uint8tableuint.c:165:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uint8tableuint.c:186:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uint8tableuint.c:187:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uint8tableuint.c:229:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uintlist.c:288:10: warning: Possible null pointer dereference: last [nullPointer]
gmap-2025-07-31/src/uintlist.c:283:12: note: Assignment 'last=NULL', assigned value is 0
gmap-2025-07-31/src/uintlist.c:285:20: note: Assuming condition is false
gmap-2025-07-31/src/uintlist.c:288:10: note: Null pointer dereference
gmap-2025-07-31/src/uintlist.c:94:22: style:inconclusive: Function 'Uintlist_head_set' argument 1 names different: declaration 'list' definition 'this'. [funcArgNamesDifferent]
gmap-2025-07-31/src/uintlist.h:119:22: note: Function 'Uintlist_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2025-07-31/src/uintlist.c:94:22: note: Function 'Uintlist_head_set' argument 1 names different: declaration 'list' definition 'this'.
gmap-2025-07-31/src/uintlist.c:244:36: style: Parameter 'array' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/uintlist.c:259:5: style: Variable 'head' is not assigned a value. [unassignedVariable]
gmap-2025-07-31/src/uinttable.c:34:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/uinttable.c:163:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttable.c:184:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttable.c:202:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttable.c:203:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uintpairtable.c:36:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/uintpairtable.c:134:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttableuint.c:34:14: style: Variable 'primes' can be declared as const array [constVariable]
gmap-2025-07-31/src/uinttableuint.c:163:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttableuint.c:184:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttableuint.c:185:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttableuint.c:227:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/uinttable_rh.c:80:20: style:inconclusive: Function 'Uinttable_new' argument 1 names different: declaration 'n' definition 'hint'. [funcArgNamesDifferent]
gmap-2025-07-31/src/uinttable_rh.h:14:20: note: Function 'Uinttable_new' argument 1 names different: declaration 'n' definition 'hint'.
gmap-2025-07-31/src/uinttable_rh.c:80:20: note: Function 'Uinttable_new' argument 1 names different: declaration 'n' definition 'hint'.
gmap-2025-07-31/src/stage3.c:6684:19: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2025-07-31/src/stage3.c:6680:19: note: First condition
gmap-2025-07-31/src/stage3.c:6684:19: note: Second condition
gmap-2025-07-31/src/stage3.c:6708:19: style: The if condition is the same as the previous if condition [duplicateCondition]
gmap-2025-07-31/src/stage3.c:6704:19: note: First condition
gmap-2025-07-31/src/stage3.c:6708:19: note: Second condition
gmap-2025-07-31/src/stage3.c:4013:16: style: Condition '0&&ambig_end_length>0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:4499:16: style: Condition '0&&ambig_end_length>0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:9059:36: style: Condition 'genomejump<=0' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:9057:38: note: Assignment 'genomejump=genomedp3-genomedp5+1', assigned value is greater than 0
gmap-2025-07-31/src/stage3.c:9059:36: note: Condition 'genomejump<=0' is always false
gmap-2025-07-31/src/stage3.c:10376:11: style: Condition '0&&firstpair->querypos!=querydp3_distalgap' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:10610:11: style: Condition '0&&firstpair->querypos!=querydp5_distalgap' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:11412:11: style: Condition '1||(firstpair->querypos==querydp5&&lastpair->querypos==querydp3)' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:17858:23: style: Condition 'watsonp' is always true [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:17808:45: note: Assuming that condition '(watsonp=this_left->watsonp)==1' is not redundant
gmap-2025-07-31/src/stage3.c:17858:23: note: Condition 'watsonp' is always true
gmap-2025-07-31/src/stage3.c:17921:23: style: Condition 'watsonp' is always false [knownConditionTrueFalse]
gmap-2025-07-31/src/stage3.c:17808:45: note: Assuming that condition '(watsonp=this_left->watsonp)==1' is not redundant
gmap-2025-07-31/src/stage3.c:17921:23: note: Condition 'watsonp' is always false
gmap-2025-07-31/src/stage3.c:3627:11: warning: Either the condition 'pairs!=NULL' is redundant or there is possible null pointer dereference: pairs. [nullPointerRedundantCheck]
gmap-2025-07-31/src/stage3.c:3617:16: note: Assuming that condition 'pairs!=NULL' is not redundant
gmap-2025-07-31/src/stage3.c:3627:11: note: Null pointer dereference
gmap-2025-07-31/src/stage3.c:12418:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/stage3.c:12429:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/stage3.c:12418:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/stage3.c:18180:12: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
gmap-2025-07-31/src/stage3.c:18182:7: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/stage3.c:18180:12: note: Found duplicate branches for 'if' and 'else'.
gmap-2025-07-31/src/stage3.c:1536:5: style: Variable 'pair' is assigned an expression that holds the same value. [redundantAssignment]
gmap-2025-07-31/src/stage3.c:1510:10: note: pair is assigned '(struct Pair_TPair_T)pairs->first' here.
gmap-2025-07-31/src/stage3.c:1536:5: note: Variable 'pair' is assigned an expression that holds the same value.
gmap-2025-07-31/src/stage3.c:10687:13: style: Variable 'start' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage3.c:10670:13: note: start is assigned
gmap-2025-07-31/src/stage3.c:10687:13: note: start is overwritten
gmap-2025-07-31/src/stage3.c:10885:13: style: Variable 'start' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage3.c:10868:13: note: start is assigned
gmap-2025-07-31/src/stage3.c:10885:13: note: start is overwritten
gmap-2025-07-31/src/stage3.c:18190:8: style: Variable 'end1' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage3.c:18164:8: note: end1 is assigned
gmap-2025-07-31/src/stage3.c:18190:8: note: end1 is overwritten
gmap-2025-07-31/src/stage3.c:18191:10: style: Variable 'start2' is reassigned a value before the old one has been used. [redundantAssignment]
gmap-2025-07-31/src/stage3.c:18165:10: note: start2 is assigned
gmap-2025-07-31/src/stage3.c:18191:10: note: start2 is overwritten
gmap-2025-07-31/src/stage3.c:11624:5: style:inconclusive: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/stage3.c:11730:5: style:inconclusive: Statements following noreturn function 'abort()' will never be executed. [unreachableCode]
gmap-2025-07-31/src/stage3.c:909:29: style: Redundant pointer operation on 'matches1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:919:29: style: Redundant pointer operation on 'matches2' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:1413:30: style: Redundant pointer operation on 'g_alt' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9081:35: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9261:35: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9277:33: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9277:68: style: Redundant pointer operation on 'incompletep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9510:35: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9531:35: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9664:54: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9832:40: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9889:42: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:9920:44: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10056:40: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10097:39: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10244:52: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10244:75: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10346:56: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10346:73: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10346:96: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10347:14: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10347:35: style: Redundant pointer operation on 'ambig_splicetype' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10358:54: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10358:77: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10478:52: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10478:75: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10580:56: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10580:73: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10580:96: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10581:14: style: Redundant pointer operation on 'ambig_end_length' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10581:35: style: Redundant pointer operation on 'ambig_splicetype' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10592:54: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:10592:77: style: Redundant pointer operation on 'finalscore' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11491:41: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11500:41: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11508:49: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11508:72: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11524:29: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11613:31: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11613:48: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11614:10: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11614:33: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11614:56: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11624:37: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11624:54: style: Redundant pointer operation on 'chop_exon_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11624:70: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11625:21: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11625:44: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11720:31: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11720:48: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11721:22: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11721:45: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11721:68: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11730:37: style: Redundant pointer operation on 'knownsplicep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11730:54: style: Redundant pointer operation on 'chop_exon_p' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11730:70: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11731:21: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11731:44: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11821:44: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:11992:39: style: Redundant pointer operation on 'dynprogindex' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12070:37: style: Redundant pointer operation on 'incompletep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12070:53: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12070:76: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12105:27: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12117:42: style: Redundant pointer operation on 'incompletep' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12117:58: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12117:81: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12151:44: style: Redundant pointer operation on 'shiftp' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12151:55: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12151:78: style: Redundant pointer operation on 'dynprogindex_major' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12197:44: style: Redundant pointer operation on 'dynprogindex_minor' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12243:21: style: Redundant pointer operation on 'nmatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12243:45: style: Redundant pointer operation on 'nmismatches' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12244:19: style: Redundant pointer operation on 'nsemicanonical' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:12244:38: style: Redundant pointer operation on 'nnoncanonical' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13806:43: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13806:66: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13806:89: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13855:42: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13855:65: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13855:88: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13952:41: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13952:64: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:13952:87: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:14001:40: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:14001:63: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:14001:86: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:15465:42: style: Redundant pointer operation on 'ambig_end_length_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:15465:65: style: Redundant pointer operation on 'ambig_splicetype_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:15465:88: style: Redundant pointer operation on 'ambig_prob_5' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:15493:40: style: Redundant pointer operation on 'ambig_end_length_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:15493:63: style: Redundant pointer operation on 'ambig_splicetype_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:15493:86: style: Redundant pointer operation on 'ambig_prob_3' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16324:41: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16324:60: style: Redundant pointer operation on 'sensedir' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16391:40: style: Redundant pointer operation on 'ambig_end_length_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16391:65: style: Redundant pointer operation on 'ambig_end_length_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16392:7: style: Redundant pointer operation on 'ambig_splicetype_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16392:32: style: Redundant pointer operation on 'ambig_splicetype_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16393:7: style: Redundant pointer operation on 'ambig_prob_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16393:26: style: Redundant pointer operation on 'ambig_prob_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16394:21: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16399:49: style: Redundant pointer operation on 'max_match_length_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16401:31: style: Redundant pointer operation on 'npairs1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16401:43: style: Redundant pointer operation on 'finalpairs1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16404:40: style: Redundant pointer operation on 'matches1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16404:53: style: Redundant pointer operation on 'unknowns1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16404:67: style: Redundant pointer operation on 'mismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16405:12: style: Redundant pointer operation on 'qopens1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16405:24: style: Redundant pointer operation on 'qindels1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16405:37: style: Redundant pointer operation on 'topens1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16405:49: style: Redundant pointer operation on 'tindels1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16406:12: style: Redundant pointer operation on 'ncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16406:28: style: Redundant pointer operation on 'nsemicanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16406:48: style: Redundant pointer operation on 'nnoncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16904:41: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16904:60: style: Redundant pointer operation on 'sensedir' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16971:40: style: Redundant pointer operation on 'ambig_end_length_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16971:65: style: Redundant pointer operation on 'ambig_end_length_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16972:7: style: Redundant pointer operation on 'ambig_splicetype_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16972:32: style: Redundant pointer operation on 'ambig_splicetype_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16973:7: style: Redundant pointer operation on 'ambig_prob_5_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16973:26: style: Redundant pointer operation on 'ambig_prob_3_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16974:21: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16979:49: style: Redundant pointer operation on 'max_match_length_1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16981:31: style: Redundant pointer operation on 'npairs1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16981:43: style: Redundant pointer operation on 'finalpairs1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16984:40: style: Redundant pointer operation on 'matches1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16984:53: style: Redundant pointer operation on 'unknowns1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16984:67: style: Redundant pointer operation on 'mismatches1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16985:12: style: Redundant pointer operation on 'qopens1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16985:24: style: Redundant pointer operation on 'qindels1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16985:37: style: Redundant pointer operation on 'topens1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16985:49: style: Redundant pointer operation on 'tindels1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16986:12: style: Redundant pointer operation on 'ncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16986:28: style: Redundant pointer operation on 'nsemicanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:16986:48: style: Redundant pointer operation on 'nnoncanonical1' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:17018:25: style: Redundant pointer operation on 'npairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:17018:36: style: Redundant pointer operation on 'pairs' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:17245:19: style: Redundant pointer operation on 'new_left' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:17246:19: style: Redundant pointer operation on 'new_right' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:18042:31: style: Redundant pointer operation on 'cdna_direction' - it's already a pointer. [redundantPointerOp]
gmap-2025-07-31/src/stage3.c:6361:108: style:inconclusive: Function 'Stage3_print_pslformat_nt' argument 5 names different: declaration 'queryseq' definition 'queryaaseq'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage3.h:243:108: note: Function 'Stage3_print_pslformat_nt' argument 5 names different: declaration 'queryseq' definition 'queryaaseq'.
gmap-2025-07-31/src/stage3.c:6361:108: note: Function 'Stage3_print_pslformat_nt' argument 5 names different: declaration 'queryseq' definition 'queryaaseq'.
gmap-2025-07-31/src/stage3.c:16426:65: style:inconclusive: Function 'Stage3_compute_one' argument 3 names different: declaration 'pairs1' definition 'finalpairs1'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage3.h:346:15: note: Function 'Stage3_compute_one' argument 3 names different: declaration 'pairs1' definition 'finalpairs1'.
gmap-2025-07-31/src/stage3.c:16426:65: note: Function 'Stage3_compute_one' argument 3 names different: declaration 'pairs1' definition 'finalpairs1'.
gmap-2025-07-31/src/stage3.c:17031:9: style:inconclusive: Function 'Stage3_mergeable' argument 3 names different: declaration 'exonexonpos' definition 'breakpoint'. [funcArgNamesDifferent]
gmap-2025-07-31/src/stage3.h:372:64: note: Function 'Stage3_mergeable' argument 3 names different: declaration 'exonexonpos' definition 'breakpoint'.
gmap-2025-07-31/src/stage3.c:17031:9: note: Function 'Stage3_mergeable' argument 3 names different: declaration 'exonexonpos' definition 'breakpoint'.
gmap-2025-07-31/src/stage3.c:787:33: style: Parameter 'alias_start' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:787:59: style: Parameter 'alias_end' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:1438:40: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:1438:60: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:1855:72: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:2237:36: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:6647:57: style: Parameter 'map_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:6741:62: style: Parameter 'map_divint_crosstable' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:11063:14: style: Parameter 'queryseq_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:11063:34: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:15417:24: style: Parameter 'cdna_direction' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:17005:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
gmap-2025-07-31/src/stage3.c:17264:34: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:17460:33: style: Parameter 'queryuc_ptr' can be declared as pointer to const [constParameterPointer]
gmap-2025-07-31/src/stage3.c:16817:34: warning: Uninitialized variable: defect_rate_fwd [uninitvar]
gmap-2025-07-31/src/stage3.c:16532:17: note: Assuming condition is true
gmap-2025-07-31/src/stage3.c:16817:34: note: Uninitialized variable: defect_rate_fwd
gmap-2025-07-31/src/stage3.c:16827:34: warning: Uninitialized variable: defect_rate_rev [uninitvar]
gmap-2025-07-31/src/stage3.c:16551:17: note: Assuming condition is true
gmap-2025-07-31/src/stage3.c:16827:34: note: Uninitialized variable: defect_rate_rev
gmap-2025-07-31/src/stage3.c:6668:22: style: Variable 'chrpos1' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:6669:23: style: Variable 'chrpos2' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:6673:23: style: Variable 'chrpos1' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:6674:22: style: Variable 'chrpos2' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9605:30: style: Variable 'acceptable_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9607:30: style: Variable 'acceptable_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9609:30: style: Variable 'acceptable_nmismatches' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9623:9: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9626:9: style: Variable 'pair' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9730:46: style: Variable 'left_goodness' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9730:66: style: Variable 'right_goodness' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9984:20: style: Variable 'middle_exonlength' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:9988:20: style: Variable 'middle_exonlength' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:10116:22: style: Variable 'single_goodness' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:10296:19: style: Variable 'protectedp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:10534:19: style: Variable 'protectedp' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:12509:11: style: Variable 'path1' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:12518:11: style: Variable 'path2' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:15426:22: style: Variable 'knownsplice5p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:15426:45: style: Variable 'knownsplice3p' is assigned a value that is never used. [unreadVariable]
gmap-2025-07-31/src/stage3.c:17070:18: style: Variable 'watsonp' is assigned a value that is never used. [unreadVariable]
diff:
head gmap-2025-07-31/src/chrom.c:373:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/filestring.c:244:17: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/filestring.c:624:17: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/localdb-read.c:2022:72: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/sarray-write.c:1032:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1032:5: note: Null pointer dereference
2.18.0 gmap-2025-07-31/src/sarray-write.c:1032:5: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1032:5: note: Null pointer dereference
head gmap-2025-07-31/src/sarray-write.c:1036:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1036:10: note: Null pointer dereference
2.18.0 gmap-2025-07-31/src/sarray-write.c:1036:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1017:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1036:10: note: Null pointer dereference
head gmap-2025-07-31/src/sarray-write.c:1256:5: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1256:5: note: Null pointer dereference
2.18.0 gmap-2025-07-31/src/sarray-write.c:1256:5: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1256:5: note: Null pointer dereference
head gmap-2025-07-31/src/sarray-write.c:1260:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1260:10: note: Null pointer dereference
2.18.0 gmap-2025-07-31/src/sarray-write.c:1260:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assuming allocation function fails
     gmap-2025-07-31/src/sarray-write.c:1241:13: note: Assignment 'fp=fopen(sarrayfile,"rb")', assigned value is 0
     gmap-2025-07-31/src/sarray-write.c:1260:10: note: Null pointer dereference
head gmap-2025-07-31/src/sequence.c:1699:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/stage2.c:5733:10: warning: Uninitialized variable: ncovered [uninitvar]
     gmap-2025-07-31/src/stage2.c:5653:57: note: Assuming condition is false
     gmap-2025-07-31/src/stage2.c:5733:10: note: Uninitialized variable: ncovered
head gmap-2025-07-31/src/tableint.c:266:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/tableuint.c:232:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/tableuint8.c:238:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/translation.c:2281:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/translation.c:2328:18: style: Variable 'this' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/uint8tableuint.c:165:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/uint8tableuint.c:229:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/uintpairtable.c:134:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/uinttable.c:163:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/uinttable.c:184:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/uinttableuint.c:163:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
head gmap-2025-07-31/src/uinttableuint.c:227:19: style: Variable 'p' can be declared as pointer to const [constVariablePointer]


DONE