2021-09-21 16:01 ftp://ftp.de.debian.org/debian/pool/main/s/subread/subread_2.0.3+dfsg.orig.tar.xz cppcheck-options: --library=posix --library=gnu --library=zlib -j4 --showtime=top5 --check-library --inconclusive --enable=style,information --template=daca2 -rp=temp -D__GNUC__ --platform=unix64 temp platform: Linux-5.10.0-8-amd64-x86_64-with-glibc2.31 python: 3.9.2 client-version: 1.3.12 compiler: g++ (Debian 10.2.1-6) 10.2.1 20210110 cppcheck: head 2.5 head-info: 47ea670eb (2021-09-20 21:27:05 +0200) count: 856 TO! elapsed-time: 63.0 1800.0 head-timing-info: Overall time: 0s old-timing-info: head results: subread-2.0.3-source/src/core-bigtable.c:84:66: style:inconclusive: Function 'init_bigtable_results' argument 2 names different: declaration 'is_rewind' definition 'is_rewinding'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-bigtable.h:14:66: note: Function 'init_bigtable_results' argument 2 names different: declaration 'is_rewind' definition 'is_rewinding'. subread-2.0.3-source/src/core-bigtable.c:84:66: note: Function 'init_bigtable_results' argument 2 names different: declaration 'is_rewind' definition 'is_rewinding'. subread-2.0.3-source/src/core-bigtable.c:302:31: style:inconclusive: Function 'bktable_free_ptrs' argument 1 names different: declaration 'bkey' definition 'bukey'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-bigtable.h:39:31: note: Function 'bktable_free_ptrs' argument 1 names different: declaration 'bkey' definition 'bukey'. subread-2.0.3-source/src/core-bigtable.c:302:31: note: Function 'bktable_free_ptrs' argument 1 names different: declaration 'bkey' definition 'bukey'. subread-2.0.3-source/src/core-bigtable.c:189:14: warning: String literal compared with variable 'NULL'. Did you intend to use strcmp() instead? [literalWithCharPtrCompare] subread-2.0.3-source/src/SUBindel.c:54:43: style: Condition 'context->input_reads.avg_read_length<0' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/SUBindel.c:53:43: note: Assignment 'context->input_reads.avg_read_length=200', assigned value is 200 subread-2.0.3-source/src/SUBindel.c:54:43: note: Condition 'context->input_reads.avg_read_length<0' is always false subread-2.0.3-source/src/SUBindel.c:55:43: style: Condition 'context->input_reads.avg_read_length<0' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/SUBindel.c:53:43: note: Assignment 'context->input_reads.avg_read_length=200', assigned value is 200 subread-2.0.3-source/src/SUBindel.c:55:43: note: Condition 'context->input_reads.avg_read_length<0' is always false subread-2.0.3-source/src/core-interface-aligner.c:658:68: style: Same expression on both sides of '-'. [duplicateExpression] subread-2.0.3-source/src/core-interface-subjunc.c:631:72: style: Expression is always false because 'else if' condition matches previous condition at line 603. [multiCondition] subread-2.0.3-source/src/core-interface-subjunc.c:681:68: style: Same expression on both sides of '-'. [duplicateExpression] subread-2.0.3-source/src/HelperFunctions.c:2776:2: warning: Return value of function pthread_mutex_trylock() is not used. [ignoredReturnValue] subread-2.0.3-source/src/HelperFunctions.c:1965:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/HelperFunctions.c:2797:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/HelperFunctions.c:2163:9: style: Condition '!(res>tmp)' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/HelperFunctions.c:2160:9: note: res is assigned 'tmp-1' here. subread-2.0.3-source/src/HelperFunctions.c:2163:9: note: Condition '!(res>tmp)' is always true subread-2.0.3-source/src/HelperFunctions.c:1072:3: error: Memory leak: file_line [memleak] subread-2.0.3-source/src/HelperFunctions.c:313:7: error: Common realloc mistake: 'bin_block' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/HelperFunctions.c:1104:30: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/HelperFunctions.c:1101:17: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/HelperFunctions.c:1104:30: note: Null pointer dereference subread-2.0.3-source/src/HelperFunctions.c:1105:30: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/HelperFunctions.c:1101:36: note: Assuming that condition 'end_ptr==NULL' is not redundant subread-2.0.3-source/src/HelperFunctions.c:1105:30: note: Null pointer dereference subread-2.0.3-source/src/HelperFunctions.c:1107:16: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/HelperFunctions.c:1101:17: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/HelperFunctions.c:1107:16: note: Null pointer dereference subread-2.0.3-source/src/HelperFunctions.c:1141:31: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/HelperFunctions.c:1138:18: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/HelperFunctions.c:1141:31: note: Null pointer dereference subread-2.0.3-source/src/HelperFunctions.c:1142:31: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/HelperFunctions.c:1138:37: note: Assuming that condition 'end_ptr==NULL' is not redundant subread-2.0.3-source/src/HelperFunctions.c:1142:31: note: Null pointer dereference subread-2.0.3-source/src/HelperFunctions.c:1145:17: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/HelperFunctions.c:1138:18: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/HelperFunctions.c:1145:17: note: Null pointer dereference subread-2.0.3-source/src/HelperFunctions.c:2735:18: style: Checking if unsigned expression 'cached_mem' is less than zero. [unsignedLessThanZero] subread-2.0.3-source/src/HelperFunctions.c:969:28: style:inconclusive: Function 'mac_or_rand_str' argument 1 names different: declaration 'char_14' definition 'str_buff'. [funcArgNamesDifferent] subread-2.0.3-source/src/HelperFunctions.h:124:28: note: Function 'mac_or_rand_str' argument 1 names different: declaration 'char_14' definition 'str_buff'. subread-2.0.3-source/src/HelperFunctions.c:969:28: note: Function 'mac_or_rand_str' argument 1 names different: declaration 'char_14' definition 'str_buff'. subread-2.0.3-source/src/HelperFunctions.c:1015:112: style:inconclusive: Function 'fast_fisher_test_one_side' argument 5 names different: declaration 'frac_buffer' definition 'buff'. [funcArgNamesDifferent] subread-2.0.3-source/src/HelperFunctions.h:126:112: note: Function 'fast_fisher_test_one_side' argument 5 names different: declaration 'frac_buffer' definition 'buff'. subread-2.0.3-source/src/HelperFunctions.c:1015:112: note: Function 'fast_fisher_test_one_side' argument 5 names different: declaration 'frac_buffer' definition 'buff'. subread-2.0.3-source/src/HelperFunctions.c:1015:122: style:inconclusive: Function 'fast_fisher_test_one_side' argument 6 names different: declaration 'buffer_size' definition 'buflen'. [funcArgNamesDifferent] subread-2.0.3-source/src/HelperFunctions.h:126:129: note: Function 'fast_fisher_test_one_side' argument 6 names different: declaration 'buffer_size' definition 'buflen'. subread-2.0.3-source/src/HelperFunctions.c:1015:122: note: Function 'fast_fisher_test_one_side' argument 6 names different: declaration 'buffer_size' definition 'buflen'. subread-2.0.3-source/src/HelperFunctions.c:2112:54: style:inconclusive: Function 'TNbignum_to_string' argument 3 names different: declaration 'maxsize' definition 'nbytes'. [funcArgNamesDifferent] subread-2.0.3-source/src/HelperFunctions.h:246:54: note: Function 'TNbignum_to_string' argument 3 names different: declaration 'maxsize' definition 'nbytes'. subread-2.0.3-source/src/HelperFunctions.c:2112:54: note: Function 'TNbignum_to_string' argument 3 names different: declaration 'maxsize' definition 'nbytes'. subread-2.0.3-source/src/HelperFunctions.c:1076:49: style: Local variable 'is_negative_strand' shadows outer argument [shadowArgument] subread-2.0.3-source/src/HelperFunctions.c:1064:139: note: Shadowed declaration subread-2.0.3-source/src/HelperFunctions.c:1076:49: note: Shadow variable subread-2.0.3-source/src/HelperFunctions.c:1077:70: style: Local variable 'chro_name' shadows outer argument [shadowArgument] subread-2.0.3-source/src/HelperFunctions.c:1064:86: note: Shadowed declaration subread-2.0.3-source/src/HelperFunctions.c:1077:70: note: Shadow variable subread-2.0.3-source/src/HelperFunctions.c:1081:16: style: Local variable 'start' shadows outer argument [shadowArgument] subread-2.0.3-source/src/HelperFunctions.c:1064:110: note: Shadowed declaration subread-2.0.3-source/src/HelperFunctions.c:1081:16: note: Shadow variable subread-2.0.3-source/src/HelperFunctions.c:1081:27: style: Local variable 'end' shadows outer argument [shadowArgument] subread-2.0.3-source/src/HelperFunctions.c:1064:130: note: Shadowed declaration subread-2.0.3-source/src/HelperFunctions.c:1081:27: note: Shadow variable subread-2.0.3-source/src/HelperFunctions.c:1868:16: style: Variable 'c' can be declared with const [constVariable] subread-2.0.3-source/src/HelperFunctions.c:1869:16: style: Variable 'd' can be declared with const [constVariable] subread-2.0.3-source/src/HelperFunctions.c:184:65: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/HelperFunctions.c:1867:16: style: Variable 'b' can be declared with const [constVariable] subread-2.0.3-source/src/HelperFunctions.c:1866:16: style: Variable 'a' can be declared with const [constVariable] subread-2.0.3-source/src/HelperFunctions.c:143:23: error: Uninitialized variable: jump_mode [uninitvar] subread-2.0.3-source/src/HelperFunctions.c:791:10: style: Variable 'ret' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/HelperFunctions.c:2831:14: style: Variable 'x' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/SNPCalling.c:1350:20: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled] subread-2.0.3-source/src/SNPCalling.c:625:2: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/SNPCalling.c:678:3: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/SNPCalling.c:872:7: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/SNPCalling.c:918:6: warning: %d in format string (no. 7) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/SNPCalling.c:651:3: error: Memory leak: snp_voting_piles [memleak] subread-2.0.3-source/src/SNPCalling.c:651:3: error: Memory leak: pcutoff_list [memleak] subread-2.0.3-source/src/SNPCalling.c:651:3: error: Memory leak: snp_filter_background_unmatched [memleak] subread-2.0.3-source/src/SNPCalling.c:651:3: error: Memory leak: snp_filter_background_matched [memleak] subread-2.0.3-source/src/SNPCalling.c:651:3: error: Memory leak: sprint_line [memleak] subread-2.0.3-source/src/SNPCalling.c:687:10: warning: Either the condition 'tmp_fp' is redundant or there is possible null pointer dereference: tmp_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:680:6: note: Assuming that condition 'tmp_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:687:10: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1129:36: warning: Either the condition '!fp' is redundant or there is possible null pointer dereference: fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1131:5: note: Assuming that condition '!fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1129:36: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1199:33: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1199:33: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1200:10: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1200:10: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1201:227: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1201:227: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1202:77: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1202:77: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1203:128: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1203:128: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1204:126: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1204:126: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1205:135: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1205:135: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1206:106: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1206:106: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1207:110: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1207:110: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:1208:59: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/SNPCalling.c:1208:59: note: Null pointer dereference subread-2.0.3-source/src/SNPCalling.c:338:23: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS] subread-2.0.3-source/src/SNPCalling.c:303:8: style: Local variable 'rlen' shadows outer variable [shadowVariable] subread-2.0.3-source/src/SNPCalling.c:269:34: note: Shadowed declaration subread-2.0.3-source/src/SNPCalling.c:303:8: note: Shadow variable subread-2.0.3-source/src/SNPCalling.c:765:17: style: Local variable 'reference_len_long' shadows outer variable [shadowVariable] subread-2.0.3-source/src/SNPCalling.c:622:16: note: Shadowed declaration subread-2.0.3-source/src/SNPCalling.c:765:17: note: Shadow variable subread-2.0.3-source/src/SNPCalling.c:210:26: style: Parameter 'bm' can be declared with const [constParameter] subread-2.0.3-source/src/SNPCalling.c:259:190: style: Parameter 'referenced_genome' can be declared with const [constParameter] subread-2.0.3-source/src/SNPCalling.c:451:83: style: Parameter 'snp_voting_piles' can be declared with const [constParameter] subread-2.0.3-source/src/SNPCalling.c:461:163: style: Parameter 'referenced_genome' can be declared with const [constParameter] subread-2.0.3-source/src/SNPCalling.c:461:219: style: Parameter 'tumor_P' can be declared with const [constParameter] subread-2.0.3-source/src/SNPCalling.c:484:111: style: Parameter 'snp_voting_piles' can be declared with const [constParameter] subread-2.0.3-source/src/SNPCalling.c:484:136: style: Parameter 'referenced_genome' can be declared with const [constParameter] subread-2.0.3-source/src/SNPCalling.c:1039:7: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/SNPCalling.c:1046:19: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/SNPCalling.c:1049:38: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/SNPCalling.c:1051:8: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/SNPCalling.c:1058:10: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/SNPCalling.c:1086:7: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/SNPCalling.c:487:17: style: Variable 'POIbase_MM' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/SNPCalling.c:487:46: style: Variable 'POIbase_MAT' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/coverage_calc.c:218:38: warning: Either the condition 'NULL==bin_entry' is redundant or there is possible null pointer dereference: bin_entry. [nullPointerRedundantCheck] subread-2.0.3-source/src/coverage_calc.c:213:13: note: Assuming that condition 'NULL==bin_entry' is not redundant subread-2.0.3-source/src/coverage_calc.c:218:38: note: Null pointer dereference subread-2.0.3-source/src/coverage_calc.c:219:24: warning: Either the condition 'NULL==bin_entry' is redundant or there is possible null pointer dereference: bin_entry. [nullPointerRedundantCheck] subread-2.0.3-source/src/coverage_calc.c:213:13: note: Assuming that condition 'NULL==bin_entry' is not redundant subread-2.0.3-source/src/coverage_calc.c:219:24: note: Null pointer dereference subread-2.0.3-source/src/coverage_calc.c:121:10: style: Redundant initialization for 'tmp_res'. The initialized value is overwritten before it is read. [redundantInitialization] subread-2.0.3-source/src/coverage_calc.c:119:17: note: tmp_res is initialized subread-2.0.3-source/src/coverage_calc.c:121:10: note: tmp_res is overwritten subread-2.0.3-source/src/coverage_calc.c:131:10: style: Variable 'tmp_res' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/coverage_calc.c:130:10: note: tmp_res is assigned subread-2.0.3-source/src/coverage_calc.c:131:10: note: tmp_res is overwritten subread-2.0.3-source/src/coverage_calc.c:135:10: style: Variable 'tmp_res' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/coverage_calc.c:134:10: note: tmp_res is assigned subread-2.0.3-source/src/coverage_calc.c:135:10: note: tmp_res is overwritten subread-2.0.3-source/src/coverage_calc.c:136:10: style: Variable 'tmp_res' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/coverage_calc.c:135:10: note: tmp_res is assigned subread-2.0.3-source/src/coverage_calc.c:136:10: note: tmp_res is overwritten subread-2.0.3-source/src/coverage_calc.c:277:9: style: Local variable 'x1' shadows outer variable [shadowVariable] subread-2.0.3-source/src/coverage_calc.c:182:17: note: Shadowed declaration subread-2.0.3-source/src/coverage_calc.c:277:9: note: Shadow variable subread-2.0.3-source/src/coverage_calc.c:309:11: style: Local variable 'chro' shadows outer variable [shadowVariable] subread-2.0.3-source/src/coverage_calc.c:166:22: note: Shadowed declaration subread-2.0.3-source/src/coverage_calc.c:309:11: note: Shadow variable subread-2.0.3-source/src/detection-calls.c:117:6: error: Common realloc mistake: 'base_2bits' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/detection-calls.c:159:47: style: Parameter 'hashed_obj' can be declared with const [constParameter] subread-2.0.3-source/src/filterJunctionTable.c:104:28: style: Parameter 'argv' can be declared with const [constParameter] subread-2.0.3-source/src/fullscan.c:68:28: style: Parameter 'c1' can be declared with const [constParameter] subread-2.0.3-source/src/fullscan.c:68:39: style: Parameter 'c2' can be declared with const [constParameter] subread-2.0.3-source/src/gen_rand_reads.c:808:5: error: Common realloc mistake: 'lbuf' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/gen_rand_reads.c:681:24: warning: Either the condition 'NULL==seqexp_str' is redundant or there is possible null pointer dereference: seqexp_str. [nullPointerRedundantCheck] subread-2.0.3-source/src/gen_rand_reads.c:677:11: note: Assuming that condition 'NULL==seqexp_str' is not redundant subread-2.0.3-source/src/gen_rand_reads.c:681:24: note: Null pointer dereference subread-2.0.3-source/src/gen_rand_reads.c:997:7: style: Local variable 'ret' shadows outer variable [shadowVariable] subread-2.0.3-source/src/gen_rand_reads.c:985:6: note: Shadowed declaration subread-2.0.3-source/src/gen_rand_reads.c:997:7: note: Shadow variable subread-2.0.3-source/src/gen_rand_reads.c:159:61: style: Parameter 'qua' can be declared with const [constParameter] subread-2.0.3-source/src/gen_rand_reads.c:1000:7: style: Variable 'ret' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/gene-algorithms.c:1749:25: style: Condition 'path_i>=0' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/gene-algorithms.c:1722:26: note: Assuming that condition 'path_i<0' is not redundant subread-2.0.3-source/src/gene-algorithms.c:1749:25: note: Condition 'path_i>=0' is always true subread-2.0.3-source/src/gene-algorithms.c:1753:25: style: Condition 'path_j>=0' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/gene-algorithms.c:1722:12: note: Assuming that condition 'path_j<0' is not redundant subread-2.0.3-source/src/gene-algorithms.c:1753:25: note: Condition 'path_j>=0' is always true subread-2.0.3-source/src/gene-algorithms.c:1760:7: style: Condition '!found' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/gene-algorithms.c:1746:14: note: Assignment 'found=0', assigned value is 0 subread-2.0.3-source/src/gene-algorithms.c:1760:7: note: Condition '!found' is always true subread-2.0.3-source/src/gene-algorithms.c:2456:28: style: Condition 'read_cursor=last_confirmed_read_pos' is not redundant subread-2.0.3-source/src/gene-algorithms.c:2456:28: note: Condition 'read_cursor200+350-1' is redundant or the array 'inserted_sequence[550]' is accessed at index 550, which is out of bounds. [arrayIndexOutOfBoundsCond] subread-2.0.3-source/src/core-indel.c:2646:22: note: Assuming that condition 'inserted_length>200+350-1' is not redundant subread-2.0.3-source/src/core-indel.c:2649:21: note: Array index out of bounds subread-2.0.3-source/src/core-indel.c:1874:26: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] subread-2.0.3-source/src/core-indel.c:1881:25: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] subread-2.0.3-source/src/core-indel.c:4694:22: style: Expression is always true because 'else if' condition is opposite to previous condition at line 4689. [multiCondition] subread-2.0.3-source/src/core-indel.c:4689:22: note: first condition subread-2.0.3-source/src/core-indel.c:4694:22: note: else if condition is opposite to first condition subread-2.0.3-source/src/core-indel.c:3757:5: warning: Identical condition '!tmp_fp', second condition is always false [identicalConditionAfterEarlyExit] subread-2.0.3-source/src/core-indel.c:3710:5: note: If condition '!tmp_fp' is true, the function will return/exit subread-2.0.3-source/src/core-indel.c:3757:5: note: Testing identical condition '!tmp_fp' subread-2.0.3-source/src/core-indel.c:1948:98: style: Condition 'total_mismatch<=2' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core-indel.c:1948:22: note: Assuming that condition 'total_mismatch<=2' is not redundant subread-2.0.3-source/src/core-indel.c:1948:98: note: Condition 'total_mismatch<=2' is always false subread-2.0.3-source/src/core-indel.c:2069:18: style: Condition 'score>best_score' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core-indel.c:2065:21: note: best_score is assigned 'score' here. subread-2.0.3-source/src/core-indel.c:2069:18: note: Condition 'score>best_score' is always false subread-2.0.3-source/src/core-indel.c:2838:8: style: Condition 'is_test_target' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core-indel.c:2798:23: note: Assignment 'is_test_target=0', assigned value is 0 subread-2.0.3-source/src/core-indel.c:2838:8: note: Condition 'is_test_target' is always false subread-2.0.3-source/src/core-indel.c:2854:5: style: Condition 'is_test_target' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core-indel.c:2798:23: note: Assignment 'is_test_target=0', assigned value is 0 subread-2.0.3-source/src/core-indel.c:2854:5: note: Condition 'is_test_target' is always false subread-2.0.3-source/src/core-indel.c:2862:5: style: Condition 'is_test_target' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core-indel.c:2798:23: note: Assignment 'is_test_target=0', assigned value is 0 subread-2.0.3-source/src/core-indel.c:2862:5: note: Condition 'is_test_target' is always false subread-2.0.3-source/src/core-indel.c:2892:5: style: Condition 'is_test_target' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core-indel.c:2798:23: note: Assignment 'is_test_target=0', assigned value is 0 subread-2.0.3-source/src/core-indel.c:2892:5: note: Condition 'is_test_target' is always false subread-2.0.3-source/src/core-indel.c:2320:20: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-indel.c:4152:9: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-indel.c:4152:9: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-indel.c:4154:9: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-indel.c:4154:9: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-indel.c:4289:4: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-indel.c:185:35: error: Memory leak: cancelled_event_list [memleak] subread-2.0.3-source/src/core-indel.c:718:4: error: Memory leak: indel_thread_context [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: read_text [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: qual_text [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: window_center_read_no [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: window_base_number [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: window_center_read_qual [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: window_center_read_masks [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: first_half_alleles [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: second_half_alleles [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: mapquality_lower_bounds_certain [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: box_read_number_certain [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: mapquality_lower_bounds [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: box_read_number [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: full_rebuilt_window [memleak] subread-2.0.3-source/src/core-indel.c:473:4: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:486:5: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:499:7: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:545:8: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:562:7: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:890:3: error: Common realloc mistake: 'records' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:1037:6: error: Common realloc mistake: 'records' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:1046:4: error: Common realloc mistake: 'records' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:1075:7: error: Common realloc mistake: 'merge_target' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: block_context.voting_indexes [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: block_context.start_keys [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: block_context.start_offsets [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: block_context.read_no_counter [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: block_context.read_rectify_space [memleak] subread-2.0.3-source/src/core-indel.c:3757:14: error: Memory leak: block_context.final_alleles [memleak] subread-2.0.3-source/src/core-indel.c:3083:72: style: Same expression on both sides of '-'. [duplicateExpression] subread-2.0.3-source/src/core-indel.c:2939:33: note: 'WINDOW_SEARCH_TREE_WIDTH' is assigned value '1' here. subread-2.0.3-source/src/core-indel.c:3083:72: note: Same expression on both sides of '-'. subread-2.0.3-source/src/core-indel.c:3130:44: style: Same expression on both sides of '-'. [duplicateExpression] subread-2.0.3-source/src/core-indel.c:2939:33: note: 'WINDOW_SEARCH_TREE_WIDTH' is assigned value '1' here. subread-2.0.3-source/src/core-indel.c:3130:44: note: Same expression on both sides of '-'. subread-2.0.3-source/src/core-indel.c:549:86: style: Unsigned expression 'tested_neighbour->event_large_side-tested_neighbour->event_small_side+tested_neighbour->indel_at_junction-event_body->event_large_side+event_body->event_small_side-event_body->indel_at_junction' can't be negative so it is unnecessary to test it. [unsignedPositive] subread-2.0.3-source/src/core-indel.c:2239:50: style:inconclusive: Function 'write_indel_final_results' argument 1 names different: declaration 'context' definition 'global_context'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:169:50: note: Function 'write_indel_final_results' argument 1 names different: declaration 'context' definition 'global_context'. subread-2.0.3-source/src/core-indel.c:2239:50: note: Function 'write_indel_final_results' argument 1 names different: declaration 'context' definition 'global_context'. subread-2.0.3-source/src/core-indel.c:2340:45: style:inconclusive: Function 'destroy_indel_module' argument 1 names different: declaration 'context' definition 'global_context'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:163:45: note: Function 'destroy_indel_module' argument 1 names different: declaration 'context' definition 'global_context'. subread-2.0.3-source/src/core-indel.c:2340:45: note: Function 'destroy_indel_module' argument 1 names different: declaration 'context' definition 'global_context'. subread-2.0.3-source/src/core-indel.c:2471:122: style:inconclusive: Function 'build_local_reassembly' argument 4 names different: declaration 'read_name_1' definition 'read_name'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:122: note: Function 'build_local_reassembly' argument 4 names different: declaration 'read_name_1' definition 'read_name'. subread-2.0.3-source/src/core-indel.c:2471:122: note: Function 'build_local_reassembly' argument 4 names different: declaration 'read_name_1' definition 'read_name'. subread-2.0.3-source/src/core-indel.c:2471:141: style:inconclusive: Function 'build_local_reassembly' argument 5 names different: declaration 'read_text_1' definition 'read_text'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:143: note: Function 'build_local_reassembly' argument 5 names different: declaration 'read_text_1' definition 'read_text'. subread-2.0.3-source/src/core-indel.c:2471:141: note: Function 'build_local_reassembly' argument 5 names different: declaration 'read_text_1' definition 'read_text'. subread-2.0.3-source/src/core-indel.c:2471:159: style:inconclusive: Function 'build_local_reassembly' argument 6 names different: declaration 'qual_text_1' definition 'qual_text'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:163: note: Function 'build_local_reassembly' argument 6 names different: declaration 'qual_text_1' definition 'qual_text'. subread-2.0.3-source/src/core-indel.c:2471:159: note: Function 'build_local_reassembly' argument 6 names different: declaration 'qual_text_1' definition 'qual_text'. subread-2.0.3-source/src/core-indel.c:2471:175: style:inconclusive: Function 'build_local_reassembly' argument 7 names different: declaration 'read_len_1' definition 'read_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:181: note: Function 'build_local_reassembly' argument 7 names different: declaration 'read_len_1' definition 'read_len'. subread-2.0.3-source/src/core-indel.c:2471:175: note: Function 'build_local_reassembly' argument 7 names different: declaration 'read_len_1' definition 'read_len'. subread-2.0.3-source/src/core-indel.c:2471:190: style:inconclusive: Function 'build_local_reassembly' argument 8 names different: declaration 'read_len_2' definition 'mate_read_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:197: note: Function 'build_local_reassembly' argument 8 names different: declaration 'read_len_2' definition 'mate_read_len'. subread-2.0.3-source/src/core-indel.c:2471:190: note: Function 'build_local_reassembly' argument 8 names different: declaration 'read_len_2' definition 'mate_read_len'. subread-2.0.3-source/src/core-indel.c:2471:248: style:inconclusive: Function 'build_local_reassembly' argument 11 names different: declaration 'is_paired_unmapped' definition 'use_mate_pos'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:251: note: Function 'build_local_reassembly' argument 11 names different: declaration 'is_paired_unmapped' definition 'use_mate_pos'. subread-2.0.3-source/src/core-indel.c:2471:248: note: Function 'build_local_reassembly' argument 11 names different: declaration 'is_paired_unmapped' definition 'use_mate_pos'. subread-2.0.3-source/src/core-indel.c:2471:280: style:inconclusive: Function 'build_local_reassembly' argument 12 names different: declaration 'current_res' definition 'current_result'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:290: note: Function 'build_local_reassembly' argument 12 names different: declaration 'current_res' definition 'current_result'. subread-2.0.3-source/src/core-indel.c:2471:280: note: Function 'build_local_reassembly' argument 12 names different: declaration 'current_res' definition 'current_result'. subread-2.0.3-source/src/core-indel.c:2471:314: style:inconclusive: Function 'build_local_reassembly' argument 13 names different: declaration 'mate_res' definition 'mate_result'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-indel.h:176:322: note: Function 'build_local_reassembly' argument 13 names different: declaration 'mate_res' definition 'mate_result'. subread-2.0.3-source/src/core-indel.c:2471:314: note: Function 'build_local_reassembly' argument 13 names different: declaration 'mate_res' definition 'mate_result'. subread-2.0.3-source/src/core-indel.c:1963:30: style: Local variable 'current_value_index' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-indel.c:1870:23: note: Shadowed declaration subread-2.0.3-source/src/core-indel.c:1963:30: note: Shadow variable subread-2.0.3-source/src/core-indel.c:2130:9: style: Local variable 'j' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-indel.c:1840:8: note: Shadowed declaration subread-2.0.3-source/src/core-indel.c:2130:9: note: Shadow variable subread-2.0.3-source/src/core-indel.c:3101:14: style: Local variable 'next_read_pos' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-indel.c:2982:9: note: Shadowed declaration subread-2.0.3-source/src/core-indel.c:3101:14: note: Shadow variable subread-2.0.3-source/src/core-indel.c:1366:40: style: Parameter 'bitmap' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:135:61: style: Parameter 'event_ids' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:261:36: style: Parameter 'ky' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:261:47: style: Parameter 'va' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:1471:107: style: Parameter 'binary_bases' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:1486:130: style: Parameter 'read_text' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:2516:141: style: Parameter 'read_text' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:3458:22: style: Parameter 'c1' can be declared with const [constParameter] subread-2.0.3-source/src/core-indel.c:3458:33: style: Parameter 'c2' can be declared with const [constParameter] subread-2.0.3-source/src/global-reassembly.c:687:7: style: Condition '!mm' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/global-reassembly.c:686:13: note: Assignment 'mm=0', assigned value is 0 subread-2.0.3-source/src/global-reassembly.c:687:7: note: Condition '!mm' is always true subread-2.0.3-source/src/global-reassembly.c:1110:3: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/global-reassembly.c:384:3: error: Memory leak: read1_tmp [memleak] subread-2.0.3-source/src/global-reassembly.c:384:3: error: Memory leak: line_buff [memleak] subread-2.0.3-source/src/global-reassembly.c:384:3: error: Memory leak: in_sequence [memleak] subread-2.0.3-source/src/global-reassembly.c:384:3: error: Memory leak: in_quality_string [memleak] subread-2.0.3-source/src/global-reassembly.c:384:3: error: Memory leak: in_readname [memleak] subread-2.0.3-source/src/global-reassembly.c:384:3: error: Resource leak: fp_fraglist [resourceLeak] subread-2.0.3-source/src/global-reassembly.c:384:3: error: Resource leak: fp_fragproperties [resourceLeak] subread-2.0.3-source/src/global-reassembly.c:402:4: error: Memory leak: read1_tmp [memleak] subread-2.0.3-source/src/global-reassembly.c:402:4: error: Memory leak: line_buff [memleak] subread-2.0.3-source/src/global-reassembly.c:402:4: error: Memory leak: in_sequence [memleak] subread-2.0.3-source/src/global-reassembly.c:402:4: error: Memory leak: in_quality_string [memleak] subread-2.0.3-source/src/global-reassembly.c:402:4: error: Memory leak: in_readname [memleak] subread-2.0.3-source/src/global-reassembly.c:402:4: error: Resource leak: fp_fraglist [resourceLeak] subread-2.0.3-source/src/global-reassembly.c:402:4: error: Resource leak: fp_fragproperties [resourceLeak] subread-2.0.3-source/src/global-reassembly.c:417:4: error: Memory leak: read1_tmp [memleak] subread-2.0.3-source/src/global-reassembly.c:417:4: error: Memory leak: line_buff [memleak] subread-2.0.3-source/src/global-reassembly.c:417:4: error: Memory leak: in_sequence [memleak] subread-2.0.3-source/src/global-reassembly.c:417:4: error: Memory leak: in_quality_string [memleak] subread-2.0.3-source/src/global-reassembly.c:417:4: error: Memory leak: in_readname [memleak] subread-2.0.3-source/src/global-reassembly.c:417:4: error: Resource leak: fp_fraglist [resourceLeak] subread-2.0.3-source/src/global-reassembly.c:417:4: error: Resource leak: fp_fragproperties [resourceLeak] subread-2.0.3-source/src/global-reassembly.c:766:48: style: Same value in both branches of ternary operator. [duplicateValueTernary] subread-2.0.3-source/src/global-reassembly.c:851:47: style: Same value in both branches of ternary operator. [duplicateValueTernary] subread-2.0.3-source/src/global-reassembly.c:1163:45: style: Same value in both branches of ternary operator. [duplicateValueTernary] subread-2.0.3-source/src/global-reassembly.c:1514:31: style: Clarify calculation precedence for '-' and '?'. [clarifyCalculation] subread-2.0.3-source/src/global-reassembly.c:1163:46: error: Memory is allocated but not initialized: seq_buf_1 [uninitdata] subread-2.0.3-source/src/global-reassembly.c:1163:36: error: Memory is allocated but not initialized: seq_buf_2 [uninitdata] subread-2.0.3-source/src/core-indel.c:2649:38: style: Variable 'inserted_sequence[inserted_length]' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/hashtable.c:952:37: style:inconclusive: Function 'isProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. [funcArgNamesDifferent] subread-2.0.3-source/src/hashtable.c:23:37: note: Function 'isProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. subread-2.0.3-source/src/hashtable.c:952:37: note: Function 'isProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. subread-2.0.3-source/src/hashtable.c:47:51: style: Parameter 'who' can be declared with const [constParameter] subread-2.0.3-source/src/hashtable.c:194:35: style: Parameter 'L_elem' can be declared with const [constParameter] subread-2.0.3-source/src/hashtable.c:194:50: style: Parameter 'R_elem' can be declared with const [constParameter] subread-2.0.3-source/src/hashtable.c:132:37: style: Parameter 'L_elem' can be declared with const [constParameter] subread-2.0.3-source/src/hashtable.c:132:52: style: Parameter 'R_elem' can be declared with const [constParameter] subread-2.0.3-source/src/hashtable.c:43:84: portability: 'ArrayListGet(arr,x1)' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/input-blc.c:38:15: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled] subread-2.0.3-source/src/input-blc.c:1053:15: style: Condition 'sample_no>0' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/input-blc.c:1049:20: note: Assignment 'sample_no=-1', assigned value is -1 subread-2.0.3-source/src/input-blc.c:1053:15: note: Condition 'sample_no>0' is always false subread-2.0.3-source/src/input-blc.c:431:2: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long long'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/input-blc.c:71:43: warning: Either the condition 'NULL==fp' is redundant or there is possible null pointer dereference: fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/input-blc.c:66:13: note: Assuming that condition 'NULL==fp' is not redundant subread-2.0.3-source/src/input-blc.c:71:43: note: Null pointer dereference subread-2.0.3-source/src/input-blc.c:266:42: style:inconclusive: Function 'cacheBCL_go_chunk_end' argument 1 names different: declaration 'blc_input' definition 'cache_input'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-blc.h:34:42: note: Function 'cacheBCL_go_chunk_end' argument 1 names different: declaration 'blc_input' definition 'cache_input'. subread-2.0.3-source/src/input-blc.c:266:42: note: Function 'cacheBCL_go_chunk_end' argument 1 names different: declaration 'blc_input' definition 'cache_input'. subread-2.0.3-source/src/input-blc.c:270:44: style:inconclusive: Function 'cacheBCL_go_chunk_start' argument 1 names different: declaration 'blc_input' definition 'cache_input'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-blc.h:33:44: note: Function 'cacheBCL_go_chunk_start' argument 1 names different: declaration 'blc_input' definition 'cache_input'. subread-2.0.3-source/src/input-blc.c:270:44: note: Function 'cacheBCL_go_chunk_start' argument 1 names different: declaration 'blc_input' definition 'cache_input'. subread-2.0.3-source/src/input-blc.c:274:35: style:inconclusive: Function 'cacheBCL_close' argument 1 names different: declaration 'blc_input' definition 'cache_input'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-blc.h:35:37: note: Function 'cacheBCL_close' argument 1 names different: declaration 'blc_input' definition 'cache_input'. subread-2.0.3-source/src/input-blc.c:274:35: note: Function 'cacheBCL_close' argument 1 names different: declaration 'blc_input' definition 'cache_input'. subread-2.0.3-source/src/input-blc.c:1064:31: style:inconclusive: Function 'cacheBCL_quality_test' argument 1 names different: declaration 'is_FASTQ_input' definition 'input_mode'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-blc.h:49:31: note: Function 'cacheBCL_quality_test' argument 1 names different: declaration 'is_FASTQ_input' definition 'input_mode'. subread-2.0.3-source/src/input-blc.c:1064:31: note: Function 'cacheBCL_quality_test' argument 1 names different: declaration 'is_FASTQ_input' definition 'input_mode'. subread-2.0.3-source/src/input-blc.c:1316:55: style:inconclusive: Function 'scBAM_next_read' argument 2 names different: declaration 'readname' definition 'read_name'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-blc.h:21:55: note: Function 'scBAM_next_read' argument 2 names different: declaration 'readname' definition 'read_name'. subread-2.0.3-source/src/input-blc.c:1316:55: note: Function 'scBAM_next_read' argument 2 names different: declaration 'readname' definition 'read_name'. subread-2.0.3-source/src/input-blc.c:1316:73: style:inconclusive: Function 'scBAM_next_read' argument 3 names different: declaration 'read' definition 'seq'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-blc.h:21:73: note: Function 'scBAM_next_read' argument 3 names different: declaration 'read' definition 'seq'. subread-2.0.3-source/src/input-blc.c:1316:73: note: Function 'scBAM_next_read' argument 3 names different: declaration 'read' definition 'seq'. subread-2.0.3-source/src/input-blc.c:1365:56: style:inconclusive: Function 'input_scBAM_init' argument 2 names different: declaration 'bam_fname' definition 'bam_fnames'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-blc.h:17:56: note: Function 'input_scBAM_init' argument 2 names different: declaration 'bam_fname' definition 'bam_fnames'. subread-2.0.3-source/src/input-blc.c:1365:56: note: Function 'input_scBAM_init' argument 2 names different: declaration 'bam_fname' definition 'bam_fnames'. subread-2.0.3-source/src/input-blc.c:867:13: style: Local variable 'xx2' shadows outer variable [shadowVariable] subread-2.0.3-source/src/input-blc.c:841:7: note: Shadowed declaration subread-2.0.3-source/src/input-blc.c:867:13: note: Shadow variable subread-2.0.3-source/src/input-blc.c:785:34: style: Parameter 's1' can be declared with const [constParameter] subread-2.0.3-source/src/input-blc.c:785:44: style: Parameter 's2' can be declared with const [constParameter] subread-2.0.3-source/src/input-blc.c:1340:36: style: Variable 'tag_type' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-blc.c:1402:7: style: Variable 'lno' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-blc.c:1515:18: style: Variable 'write_ptr' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core.c:1917:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/core.c:3718:13: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] subread-2.0.3-source/src/core.c:300:6: style: Condition 'is_R_code' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/core.c:186:15: note: Assignment 'is_R_code=1', assigned value is 1 subread-2.0.3-source/src/core.c:300:6: note: Condition 'is_R_code' is always true subread-2.0.3-source/src/core.c:810:10: style: Condition 'wret==-1' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core.c:800:13: note: Assignment 'wret=0', assigned value is 0 subread-2.0.3-source/src/core.c:810:10: note: Condition 'wret==-1' is always false subread-2.0.3-source/src/core.c:745:5: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core.c:1485:7: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core.c:4519:2: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core.c:933:3: error: Memory leak: fline [memleak] subread-2.0.3-source/src/core.c:3113:3: error: Memory leak: read_text_1 [memleak] subread-2.0.3-source/src/core.c:3113:3: error: Memory leak: read_text_2 [memleak] subread-2.0.3-source/src/core.c:3113:3: error: Memory leak: qual_text_1 [memleak] subread-2.0.3-source/src/core.c:3113:3: error: Memory leak: qual_text_2 [memleak] subread-2.0.3-source/src/core.c:3113:3: error: Memory leak: vote_1 [memleak] subread-2.0.3-source/src/core.c:3113:3: error: Memory leak: vote_2 [memleak] subread-2.0.3-source/src/core.c:3113:3: error: Memory leak: vote_fg [memleak] subread-2.0.3-source/src/core.c:239:19: style: Variable 'content_len' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/core.c:238:19: note: content_len is assigned subread-2.0.3-source/src/core.c:239:19: note: content_len is overwritten subread-2.0.3-source/src/core.c:3452:102: style: Same expression on both sides of '||'. [duplicateExpression] subread-2.0.3-source/src/core.c:3749:93: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary] subread-2.0.3-source/src/core.c:4260:86: style: Same expression on both sides of '||'. [duplicateExpression] subread-2.0.3-source/src/core.c:4270:86: style: Same expression on both sides of '||'. [duplicateExpression] subread-2.0.3-source/src/core.c:3576:42: style:inconclusive: Function 'read_chunk_circles' argument 1 names different: declaration 'context' definition 'global_context'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.h:627:43: note: Function 'read_chunk_circles' argument 1 names different: declaration 'context' definition 'global_context'. subread-2.0.3-source/src/core.c:3576:42: note: Function 'read_chunk_circles' argument 1 names different: declaration 'context' definition 'global_context'. subread-2.0.3-source/src/core.c:4497:46: style:inconclusive: Function 'term_strncpy' argument 3 names different: declaration 'max_dst_memory' definition 'max_dst_mem'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.h:660:46: note: Function 'term_strncpy' argument 3 names different: declaration 'max_dst_memory' definition 'max_dst_mem'. subread-2.0.3-source/src/core.c:4497:46: note: Function 'term_strncpy' argument 3 names different: declaration 'max_dst_memory' definition 'max_dst_mem'. subread-2.0.3-source/src/core.c:4522:257: style:inconclusive: Function 'chimeric_cigar_parts' argument 10 names different: declaration 'out_read_lens' definition 'perfect_lens'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.h:675:258: note: Function 'chimeric_cigar_parts' argument 10 names different: declaration 'out_read_lens' definition 'perfect_lens'. subread-2.0.3-source/src/core.c:4522:257: note: Function 'chimeric_cigar_parts' argument 10 names different: declaration 'out_read_lens' definition 'perfect_lens'. subread-2.0.3-source/src/core.c:4751:33: style:inconclusive: Function 'basic_sort' argument 2 names different: declaration 'arr_size' definition 'items'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.h:679:32: note: Function 'basic_sort' argument 2 names different: declaration 'arr_size' definition 'items'. subread-2.0.3-source/src/core.c:4751:33: note: Function 'basic_sort' argument 2 names different: declaration 'arr_size' definition 'items'. subread-2.0.3-source/src/core.c:4830:240: style:inconclusive: Function 'test_PE_and_same_chro_align' argument 9 names different: declaration 'rname' definition 'read_name'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.c:2419:240: note: Function 'test_PE_and_same_chro_align' argument 9 names different: declaration 'rname' definition 'read_name'. subread-2.0.3-source/src/core.c:4830:240: note: Function 'test_PE_and_same_chro_align' argument 9 names different: declaration 'rname' definition 'read_name'. subread-2.0.3-source/src/core.c:4836:154: style:inconclusive: Function 'test_PE_and_same_chro' argument 6 names different: declaration 'rlen1' definition 'read_len_1'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.h:687:155: note: Function 'test_PE_and_same_chro' argument 6 names different: declaration 'rlen1' definition 'read_len_1'. subread-2.0.3-source/src/core.c:4836:154: note: Function 'test_PE_and_same_chro' argument 6 names different: declaration 'rlen1' definition 'read_len_1'. subread-2.0.3-source/src/core.c:4836:170: style:inconclusive: Function 'test_PE_and_same_chro' argument 7 names different: declaration 'rlen2' definition 'read_len_2'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.h:687:166: note: Function 'test_PE_and_same_chro' argument 7 names different: declaration 'rlen2' definition 'read_len_2'. subread-2.0.3-source/src/core.c:4836:170: note: Function 'test_PE_and_same_chro' argument 7 names different: declaration 'rlen2' definition 'read_len_2'. subread-2.0.3-source/src/core.c:4864:25: style:inconclusive: Function 'FIXLENstrcmp' argument 1 names different: declaration 'fixed_len' definition 'flen'. [funcArgNamesDifferent] subread-2.0.3-source/src/core.h:689:25: note: Function 'FIXLENstrcmp' argument 1 names different: declaration 'fixed_len' definition 'flen'. subread-2.0.3-source/src/core.c:4864:25: note: Function 'FIXLENstrcmp' argument 1 names different: declaration 'fixed_len' definition 'flen'. subread-2.0.3-source/src/core.c:184:20: style: Local variable 'content_len' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core.c:171:6: note: Shadowed declaration subread-2.0.3-source/src/core.c:184:20: note: Shadow variable subread-2.0.3-source/src/core.c:2745:8: style: Local variable 'is_second_read' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core.c:2590:7: note: Shadowed declaration subread-2.0.3-source/src/core.c:2745:8: note: Shadow variable subread-2.0.3-source/src/core.c:4522:159: style: Parameter 'in_cigar' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:4864:38: style: Parameter 'rname' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:1231:36: style: Parameter 'CIGAR' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:1324:97: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:1349:61: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:1600:41: style: Parameter 'remainder_cigar' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:1621:46: style: Parameter 'src' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:1659:22: style: Parameter 'cig' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:4775:50: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:3057:107: style: Parameter 'qual' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:4388:30: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:4419:28: style: Parameter 'bincigar' can be declared with const [constParameter] subread-2.0.3-source/src/core.c:1081:16: error: Uninitialized variable: temp_file_name [uninitvar] subread-2.0.3-source/src/core.c:1372:29: style: Variable 'linear_cursor' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core.c:1387:19: style: Variable 'linear_cursor' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core.c:1442:25: style: Variable 'chimeric_sections' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core.c:2575:27: style: Variable 'r1_align_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory] subread-2.0.3-source/src/core.c:2576:27: style: Variable 'r2_align_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory] subread-2.0.3-source/src/core.c:2578:29: style: Variable 'r1_subjunc_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory] subread-2.0.3-source/src/core.c:2579:29: style: Variable 'r2_subjunc_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory] subread-2.0.3-source/src/core.c:259:10: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing] subread-2.0.3-source/src/core-junction.c:1371:54: error: Array 'current_vote->pos[30][24]' accessed at index current_vote->pos[-1][-1], which is out of bounds. [negativeIndex] subread-2.0.3-source/src/core-junction.c:1448:43: note: Assignment 'best_R1_j=-1', assigned value is -1 subread-2.0.3-source/src/core-junction.c:1450:21: note: Assuming condition is false subread-2.0.3-source/src/core-junction.c:1469:70: note: Calling function 'simple_copy_vote_to_result', 4th argument 'best_R1_j' value is -1 subread-2.0.3-source/src/core-junction.c:1371:54: note: Negative array index subread-2.0.3-source/src/core-junction.c:1373:132: error: Array 'current_vote->indel_recorder[30][24][21]' accessed at index current_vote->indel_recorder[-1][-1], which is out of bounds. [negativeIndex] subread-2.0.3-source/src/core-junction.c:1448:43: note: Assignment 'best_R1_j=-1', assigned value is -1 subread-2.0.3-source/src/core-junction.c:1450:21: note: Assuming condition is false subread-2.0.3-source/src/core-junction.c:1469:70: note: Calling function 'simple_copy_vote_to_result', 4th argument 'best_R1_j' value is -1 subread-2.0.3-source/src/core-junction.c:1373:132: note: Negative array index subread-2.0.3-source/src/core-junction.c:1376:52: error: Array 'current_vote->masks[30][24]' accessed at index current_vote->masks[-1][-1], which is out of bounds. [negativeIndex] subread-2.0.3-source/src/core-junction.c:1448:43: note: Assignment 'best_R1_j=-1', assigned value is -1 subread-2.0.3-source/src/core-junction.c:1450:21: note: Assuming condition is false subread-2.0.3-source/src/core-junction.c:1469:70: note: Calling function 'simple_copy_vote_to_result', 4th argument 'best_R1_j' value is -1 subread-2.0.3-source/src/core-junction.c:1376:52: note: Negative array index subread-2.0.3-source/src/core-junction.c:5205:30: style: Array index 'kk' is used before limits check. [arrayIndexThenCheck] subread-2.0.3-source/src/core-junction.c:1945:26: style: Expression is always false because 'else if' condition matches previous condition at line 1943. [multiCondition] subread-2.0.3-source/src/core-junction.c:2875:30: warning: Identical condition 'last_matched_base_index<0', second condition is always false [identicalConditionAfterEarlyExit] subread-2.0.3-source/src/core-junction.c:2872:29: note: If condition 'last_matched_base_index<0' is true, the function will return/exit subread-2.0.3-source/src/core-junction.c:2875:30: note: Testing identical condition 'last_matched_base_index<0' subread-2.0.3-source/src/core-junction.c:3372:23: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition] subread-2.0.3-source/src/core-junction.c:3361:22: note: outer condition: mismatch_bases<=applied_mismatch subread-2.0.3-source/src/core-junction.c:3372:23: note: opposite inner condition: mismatch_bases>applied_mismatch subread-2.0.3-source/src/core-junction.c:1883:19: style: Condition 'highest_score>0' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/core-junction.c:1853:45: note: Assuming that condition 'highest_score>160-159' is not redundant subread-2.0.3-source/src/core-junction.c:1883:19: note: Condition 'highest_score>0' is always true subread-2.0.3-source/src/core-junction.c:2878:30: style: Condition 'last_matched_base_index>=0' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/core-junction.c:2872:29: note: Assuming that condition 'last_matched_base_index<0' is not redundant subread-2.0.3-source/src/core-junction.c:2878:30: note: Condition 'last_matched_base_index>=0' is always true subread-2.0.3-source/src/core-junction.c:5689:21: style: Condition 'nSupD1mates>0' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/core-junction.c:5647:20: note: Assignment 'nSupD1mates=0', assigned value is 0 subread-2.0.3-source/src/core-junction.c:5689:21: note: Condition 'nSupD1mates>0' is always false subread-2.0.3-source/src/core-junction.c:3110:6: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/core-junction.c:3295:7: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:4175:4: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:4177:4: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:4179:10: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:4179:10: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/core-junction.c:4179:10: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/core-junction.c:4185:4: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:4187:4: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:4189:11: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:4189:11: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/core-junction.c:4189:11: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/core-junction.c:4263:4: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/core-junction.c:1248:26: style: Variable 'right_indel_offset' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/core-junction.c:1237:27: note: right_indel_offset is assigned subread-2.0.3-source/src/core-junction.c:1248:26: note: right_indel_offset is overwritten subread-2.0.3-source/src/core-junction.c:1248:26: style: Variable 'right_indel_offset' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/core-junction.c:1241:27: note: right_indel_offset is assigned subread-2.0.3-source/src/core-junction.c:1248:26: note: right_indel_offset is overwritten subread-2.0.3-source/src/core-junction.c:4455:12: style: Variable 'max_score' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/core-junction.c:4408:13: note: max_score is assigned subread-2.0.3-source/src/core-junction.c:4455:12: note: max_score is overwritten subread-2.0.3-source/src/core-junction.c:4850:26: style: Variable '*read_coverage_start' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/core-junction.c:4847:26: note: *read_coverage_start is assigned subread-2.0.3-source/src/core-junction.c:4850:26: note: *read_coverage_start is overwritten subread-2.0.3-source/src/core-junction.c:4851:24: style: Variable '*read_coverage_end' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/core-junction.c:4848:24: note: *read_coverage_end is assigned subread-2.0.3-source/src/core-junction.c:4851:24: note: *read_coverage_end is overwritten subread-2.0.3-source/src/core-junction.c:3264:8: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch] subread-2.0.3-source/src/core-junction.c:3271:8: note: Found duplicate branches for 'if' and 'else'. subread-2.0.3-source/src/core-junction.c:3264:8: note: Found duplicate branches for 'if' and 'else'. subread-2.0.3-source/src/long-hashtable.c:389:6: error: Common realloc mistake: 'ret' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/long-hashtable.c:117:3: style:inconclusive: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode] subread-2.0.3-source/src/long-hashtable.c:265:56: style:inconclusive: Function 'lnhash_query' argument 2 names different: declaration 'vote' definition 'votes'. [funcArgNamesDifferent] subread-2.0.3-source/src/long-hashtable.h:81:56: note: Function 'lnhash_query' argument 2 names different: declaration 'vote' definition 'votes'. subread-2.0.3-source/src/long-hashtable.c:265:56: note: Function 'lnhash_query' argument 2 names different: declaration 'vote' definition 'votes'. subread-2.0.3-source/src/core-junction.c:4155:84: style: Same expression on both sides of '-'. [duplicateExpression] subread-2.0.3-source/src/core-junction.c:4296:90: style: Same expression on both sides of '-'. [duplicateExpression] subread-2.0.3-source/src/core-junction.c:5492:39: style: Same expression on both sides of '-'. [duplicateExpression] subread-2.0.3-source/src/core-junction.c:6290:8: style: Unsigned expression 'event_body_Y->event_large_side-q_res_2->selected_position' can't be negative so it is unnecessary to test it. [unsignedPositive] subread-2.0.3-source/src/core-junction.c:586:253: style:inconclusive: Function 'search_events_to_back' argument 9 names different: declaration 'suggested_movements' definition 'suggested_movement'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:140:253: note: Function 'search_events_to_back' argument 9 names different: declaration 'suggested_movements' definition 'suggested_movement'. subread-2.0.3-source/src/core-junction.c:586:253: note: Function 'search_events_to_back' argument 9 names different: declaration 'suggested_movements' definition 'suggested_movement'. subread-2.0.3-source/src/core-junction.c:1784:333: style:inconclusive: Function 'align_cluster' argument 14 names different: declaration 'ii_path' definition 'best_ii_path'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.c:1368:333: note: Function 'align_cluster' argument 14 names different: declaration 'ii_path' definition 'best_ii_path'. subread-2.0.3-source/src/core-junction.c:1784:333: note: Function 'align_cluster' argument 14 names different: declaration 'ii_path' definition 'best_ii_path'. subread-2.0.3-source/src/core-junction.c:1784:353: style:inconclusive: Function 'align_cluster' argument 15 names different: declaration 'jj_path' definition 'best_jj_path'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.c:1368:348: note: Function 'align_cluster' argument 15 names different: declaration 'jj_path' definition 'best_jj_path'. subread-2.0.3-source/src/core-junction.c:1784:353: note: Function 'align_cluster' argument 15 names different: declaration 'jj_path' definition 'best_jj_path'. subread-2.0.3-source/src/core-junction.c:1784:373: style:inconclusive: Function 'align_cluster' argument 16 names different: declaration 'masks' definition 'best_masks'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.c:1368:363: note: Function 'align_cluster' argument 16 names different: declaration 'masks' definition 'best_masks'. subread-2.0.3-source/src/core-junction.c:1784:373: note: Function 'align_cluster' argument 16 names different: declaration 'masks' definition 'best_masks'. subread-2.0.3-source/src/core-junction.c:1784:391: style:inconclusive: Function 'align_cluster' argument 17 names different: declaration 'path_len' definition 'best_path_length'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.c:1368:376: note: Function 'align_cluster' argument 17 names different: declaration 'path_len' definition 'best_path_length'. subread-2.0.3-source/src/core-junction.c:1784:391: note: Function 'align_cluster' argument 17 names different: declaration 'path_len' definition 'best_path_length'. subread-2.0.3-source/src/core-junction.c:2610:120: style:inconclusive: Function 'explain_read' argument 3 names different: declaration 'realigns' definition 'final_realignments'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:130:120: note: Function 'explain_read' argument 3 names different: declaration 'realigns' definition 'final_realignments'. subread-2.0.3-source/src/core-junction.c:2610:120: note: Function 'explain_read' argument 3 names different: declaration 'realigns' definition 'final_realignments'. subread-2.0.3-source/src/core-junction.c:2610:231: style:inconclusive: Function 'explain_read' argument 8 names different: declaration 'qual' definition 'qual_text'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:130:220: note: Function 'explain_read' argument 8 names different: declaration 'qual' definition 'qual_text'. subread-2.0.3-source/src/core-junction.c:2610:231: note: Function 'explain_read' argument 8 names different: declaration 'qual' definition 'qual_text'. subread-2.0.3-source/src/core-junction.c:3145:167: style:inconclusive: Function 'finalise_explain_CIGAR' argument 4 names different: declaration 'realigns' definition 'final_realignments'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:138:167: note: Function 'finalise_explain_CIGAR' argument 4 names different: declaration 'realigns' definition 'final_realignments'. subread-2.0.3-source/src/core-junction.c:3145:167: note: Function 'finalise_explain_CIGAR' argument 4 names different: declaration 'realigns' definition 'final_realignments'. subread-2.0.3-source/src/core-junction.c:3507:119: style:inconclusive: Function 'is_ambiguous_voting' argument 4 names different: declaration 'max_vote' definition 'selected_vote'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:153:119: note: Function 'is_ambiguous_voting' argument 4 names different: declaration 'max_vote' definition 'selected_vote'. subread-2.0.3-source/src/core-junction.c:3507:119: note: Function 'is_ambiguous_voting' argument 4 names different: declaration 'max_vote' definition 'selected_vote'. subread-2.0.3-source/src/core-junction.c:3561:107: style:inconclusive: Function 'donor_jumped_score' argument 3 names different: declaration 'left_virtualHead_abs_offset' definition 'small_virtualHead_abs_offset'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:107: note: Function 'donor_jumped_score' argument 3 names different: declaration 'left_virtualHead_abs_offset' definition 'small_virtualHead_abs_offset'. subread-2.0.3-source/src/core-junction.c:3561:107: note: Function 'donor_jumped_score' argument 3 names different: declaration 'left_virtualHead_abs_offset' definition 'small_virtualHead_abs_offset'. subread-2.0.3-source/src/core-junction.c:3561:150: style:inconclusive: Function 'donor_jumped_score' argument 4 names different: declaration 'right_virtualHead_abs_offset' definition 'large_virtualHead_abs_offset'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:149: note: Function 'donor_jumped_score' argument 4 names different: declaration 'right_virtualHead_abs_offset' definition 'large_virtualHead_abs_offset'. subread-2.0.3-source/src/core-junction.c:3561:150: note: Function 'donor_jumped_score' argument 4 names different: declaration 'right_virtualHead_abs_offset' definition 'large_virtualHead_abs_offset'. subread-2.0.3-source/src/core-junction.c:3561:249: style:inconclusive: Function 'donor_jumped_score' argument 9 names different: declaration 'is_left_half_negative' definition 'is_small_half_negative'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:248: note: Function 'donor_jumped_score' argument 9 names different: declaration 'is_left_half_negative' definition 'is_small_half_negative'. subread-2.0.3-source/src/core-junction.c:3561:249: note: Function 'donor_jumped_score' argument 9 names different: declaration 'is_left_half_negative' definition 'is_small_half_negative'. subread-2.0.3-source/src/core-junction.c:3561:277: style:inconclusive: Function 'donor_jumped_score' argument 10 names different: declaration 'is_right_half_negative' definition 'is_large_half_negative'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:275: note: Function 'donor_jumped_score' argument 10 names different: declaration 'is_right_half_negative' definition 'is_large_half_negative'. subread-2.0.3-source/src/core-junction.c:3561:277: note: Function 'donor_jumped_score' argument 10 names different: declaration 'is_right_half_negative' definition 'is_large_half_negative'. subread-2.0.3-source/src/core-junction.c:3561:305: style:inconclusive: Function 'donor_jumped_score' argument 11 names different: declaration 'is_left_part_on_left_as_reversed' definition 'small_half_on_left_reversed'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:303: note: Function 'donor_jumped_score' argument 11 names different: declaration 'is_left_part_on_left_as_reversed' definition 'small_half_on_left_reversed'. subread-2.0.3-source/src/core-junction.c:3561:305: note: Function 'donor_jumped_score' argument 11 names different: declaration 'is_left_part_on_left_as_reversed' definition 'small_half_on_left_reversed'. subread-2.0.3-source/src/core-junction.c:3561:388: style:inconclusive: Function 'donor_jumped_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:391: note: Function 'donor_jumped_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. subread-2.0.3-source/src/core-junction.c:3561:388: note: Function 'donor_jumped_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. subread-2.0.3-source/src/core-junction.c:3561:424: style:inconclusive: Function 'donor_jumped_score' argument 15 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:413: note: Function 'donor_jumped_score' argument 15 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:3561:424: note: Function 'donor_jumped_score' argument 15 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:3561:464: style:inconclusive: Function 'donor_jumped_score' argument 16 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:148:440: note: Function 'donor_jumped_score' argument 16 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:3561:464: note: Function 'donor_jumped_score' argument 16 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:3660:176: style:inconclusive: Function 'donor_score' argument 5 names different: declaration 'left_indels' definition 'left_indel_offset'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:146:176: note: Function 'donor_score' argument 5 names different: declaration 'left_indels' definition 'left_indel_offset'. subread-2.0.3-source/src/core-junction.c:3660:176: note: Function 'donor_score' argument 5 names different: declaration 'left_indels' definition 'left_indel_offset'. subread-2.0.3-source/src/core-junction.c:3660:199: style:inconclusive: Function 'donor_score' argument 6 names different: declaration 'right_indels' definition 'right_indel_offset'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:146:193: note: Function 'donor_score' argument 6 names different: declaration 'right_indels' definition 'right_indel_offset'. subread-2.0.3-source/src/core-junction.c:3660:199: note: Function 'donor_score' argument 6 names different: declaration 'right_indels' definition 'right_indel_offset'. subread-2.0.3-source/src/core-junction.c:3660:361: style:inconclusive: Function 'donor_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:146:349: note: Function 'donor_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. subread-2.0.3-source/src/core-junction.c:3660:361: note: Function 'donor_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. subread-2.0.3-source/src/core-junction.c:3660:397: style:inconclusive: Function 'donor_score' argument 15 names different: declaration 'inserted_bases' definition 'final_inserted_bases'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:146:371: note: Function 'donor_score' argument 15 names different: declaration 'inserted_bases' definition 'final_inserted_bases'. subread-2.0.3-source/src/core-junction.c:3660:397: note: Function 'donor_score' argument 15 names different: declaration 'inserted_bases' definition 'final_inserted_bases'. subread-2.0.3-source/src/core-junction.c:3660:425: style:inconclusive: Function 'donor_score' argument 16 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:146:393: note: Function 'donor_score' argument 16 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:3660:425: note: Function 'donor_score' argument 16 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:3660:465: style:inconclusive: Function 'donor_score' argument 17 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.h:146:420: note: Function 'donor_score' argument 17 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:3660:465: note: Function 'donor_score' argument 17 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. subread-2.0.3-source/src/core-junction.c:4214:43: style:inconclusive: Function 'write_inversion_results_final' argument 1 names different: declaration 'key' definition 'bukey'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.c:4125:43: note: Function 'write_inversion_results_final' argument 1 names different: declaration 'key' definition 'bukey'. subread-2.0.3-source/src/core-junction.c:4214:43: note: Function 'write_inversion_results_final' argument 1 names different: declaration 'key' definition 'bukey'. subread-2.0.3-source/src/core-junction.c:4239:47: style:inconclusive: Function 'write_translocation_results_final' argument 1 names different: declaration 'key' definition 'bukey'. [funcArgNamesDifferent] subread-2.0.3-source/src/core-junction.c:4124:47: note: Function 'write_translocation_results_final' argument 1 names different: declaration 'key' definition 'bukey'. subread-2.0.3-source/src/core-junction.c:4239:47: note: Function 'write_translocation_results_final' argument 1 names different: declaration 'key' definition 'bukey'. subread-2.0.3-source/src/core-junction.c:1654:10: style: Local variable 'nch' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-junction.c:1604:22: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:1654:10: note: Shadow variable subread-2.0.3-source/src/core-junction.c:1663:10: style: Local variable 'nch' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-junction.c:1604:22: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:1663:10: note: Shadow variable subread-2.0.3-source/src/core-junction.c:1689:10: style: Local variable 'nch' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-junction.c:1604:22: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:1689:10: note: Shadow variable subread-2.0.3-source/src/core-junction.c:1698:10: style: Local variable 'nch' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-junction.c:1604:22: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:1698:10: note: Shadow variable subread-2.0.3-source/src/core-junction.c:2214:62: style: Local variable 'i' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-junction.c:2206:21: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:2214:62: note: Shadow variable subread-2.0.3-source/src/core-junction.c:2214:66: style: Local variable 'j' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-junction.c:2206:23: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:2214:66: note: Shadow variable subread-2.0.3-source/src/core-junction.c:2318:9: style: Local variable 'is_PE_distance' shadows outer function [shadowFunction] subread-2.0.3-source/src/core-junction.c:812:5: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:2318:9: note: Shadow variable subread-2.0.3-source/src/core-junction.c:5286:33: style: Local variable 'event_space' shadows outer variable [shadowVariable] subread-2.0.3-source/src/core-junction.c:5145:23: note: Shadowed declaration subread-2.0.3-source/src/core-junction.c:5286:33: note: Shadow variable subread-2.0.3-source/src/core-junction.c:1056:399: style: Parameter 'is_fully_covered' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:2148:134: style: Parameter 'ii_array' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:2148:150: style: Parameter 'jj_array' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:2016:38: style: Parameter 'small_bases' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:2016:58: style: Parameter 'large_bases' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:2766:141: style: Parameter 'read_text' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:3442:35: style: Parameter 'ch1' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:3442:47: style: Parameter 'ch2' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:3457:35: style: Parameter 'ch1' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:3457:47: style: Parameter 'ch2' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:4351:30: style: Parameter 'ch1' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:4351:42: style: Parameter 'ch2' can be declared with const [constParameter] subread-2.0.3-source/src/core-junction.c:4726:578: style: Parameter 'max_indel_recorder' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMbase-index.c:92:3: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/longread-one/LRMbase-index.c:97:3: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/longread-one/LRMbase-index.c:109:3: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/longread-one/LRMbase-index.c:116:3: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/longread-one/LRMbase-index.c:144:129: style:inconclusive: Function 'LRMvalidate_mapping' argument 6 names different: declaration 'rev' definition 'neg'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMbase-index.h:37:129: note: Function 'LRMvalidate_mapping' argument 6 names different: declaration 'rev' definition 'neg'. subread-2.0.3-source/src/longread-one/LRMbase-index.c:144:129: note: Function 'LRMvalidate_mapping' argument 6 names different: declaration 'rev' definition 'neg'. subread-2.0.3-source/src/longread-one/LRMbase-index.c:144:140: style:inconclusive: Function 'LRMvalidate_mapping' argument 7 names different: declaration 'mapped_length' definition 'maplen'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMbase-index.h:37:140: note: Function 'LRMvalidate_mapping' argument 7 names different: declaration 'mapped_length' definition 'maplen'. subread-2.0.3-source/src/longread-one/LRMbase-index.c:144:140: note: Function 'LRMvalidate_mapping' argument 7 names different: declaration 'mapped_length' definition 'maplen'. subread-2.0.3-source/src/longread-one/LRMbase-index.c:211:26: style: Parameter 'read' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMbase-index.c:144:69: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMbase-index.c:146:55: style: Variable 'all_mismatched' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/longread-one/LRMbase-index.c:183:20: style: Variable 'all_mismatched' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core-junction.c:5991:48: error: Memory is allocated but not initialized: s1_ptrs [uninitdata] subread-2.0.3-source/src/core-junction.c:5991:40: error: Memory is allocated but not initialized: s2_ptrs [uninitdata] subread-2.0.3-source/src/core-junction.c:6178:41: error: Memory is allocated but not initialized: s2_ptrs [uninitdata] subread-2.0.3-source/src/core-junction.c:6179:49: error: Memory is allocated but not initialized: s2_poses [uninitdata] subread-2.0.3-source/src/core-junction.c:6183:83: error: Memory is allocated but not initialized: s1_result_ptr_list [uninitdata] subread-2.0.3-source/src/core-junction.c:6183:64: error: Memory is allocated but not initialized: s2_result_ptr_list [uninitdata] subread-2.0.3-source/src/core-junction.c:48:15: style: struct member 'select_junction_record_t::piece_main_abs_offset' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:49:15: style: struct member 'select_junction_record_t::piece_minor_abs_offset' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:50:6: style: struct member 'select_junction_record_t::piece_main_masks' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:51:8: style: struct member 'select_junction_record_t::piece_main_coverage_start' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:52:8: style: struct member 'select_junction_record_t::piece_main_coverage_end' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:54:8: style: struct member 'select_junction_record_t::piece_main_hamming_match' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:55:8: style: struct member 'select_junction_record_t::piece_main_read_quality' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:56:8: style: struct member 'select_junction_record_t::piece_minor_hamming_match' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:57:8: style: struct member 'select_junction_record_t::piece_minor_read_quality' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:58:6: style: struct member 'select_junction_record_t::piece_minor_score' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:59:8: style: struct member 'select_junction_record_t::intron_length' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:61:22: style: struct member 'select_junction_record_t::piece_main_indel_record' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:62:17: style: struct member 'select_junction_record_t::piece_main_indels' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:63:17: style: struct member 'select_junction_record_t::piece_minor_indel_offset' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:64:21: style: struct member 'select_junction_record_t::piece_main_votes' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:65:21: style: struct member 'select_junction_record_t::piece_minor_votes' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:67:8: style: struct member 'select_junction_record_t::piece_minor_coverage_start' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:68:8: style: struct member 'select_junction_record_t::piece_minor_coverage_end' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:70:7: style: struct member 'select_junction_record_t::inserted_bases' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:71:7: style: struct member 'select_junction_record_t::is_GT_AG_donors' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:74:7: style: struct member 'select_junction_record_t::is_break_even' is never used. [unusedStructMember] subread-2.0.3-source/src/core-junction.c:2809:47: style: Variable 'removed_base_index' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core-junction.c:3151:28: style: Variable 'to_be_supported_count' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core-junction.c:3153:37: style: Variable 'total_perfect_matched_sections' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core-junction.c:3242:36: style: Variable 'total_perfect_matched_sections' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core-junction.c:4984:21: style: Variable 'best_select_votes' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core-junction.c:5142:20: style: Variable 'window_cursor' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/core-junction.c:5786:14: style: Variable 'found_PQR' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/index-builder.c:98:3: error: Memory leak: read_offsets [memleak] subread-2.0.3-source/src/index-builder.c:98:3: error: Memory leak: read_names [memleak] subread-2.0.3-source/src/index-builder.c:98:3: error: Memory leak: ginp [memleak] subread-2.0.3-source/src/index-builder.c:104:3: error: Memory leak: read_offsets [memleak] subread-2.0.3-source/src/index-builder.c:104:3: error: Memory leak: read_names [memleak] subread-2.0.3-source/src/index-builder.c:104:3: error: Memory leak: ginp [memleak] subread-2.0.3-source/src/index-builder.c:110:3: error: Memory leak: read_offsets [memleak] subread-2.0.3-source/src/index-builder.c:110:3: error: Memory leak: read_names [memleak] subread-2.0.3-source/src/index-builder.c:110:3: error: Memory leak: ginp [memleak] subread-2.0.3-source/src/index-builder.c:117:115: error: Memory leak: read_offsets [memleak] subread-2.0.3-source/src/index-builder.c:117:115: error: Memory leak: read_names [memleak] subread-2.0.3-source/src/index-builder.c:117:115: error: Memory leak: ginp [memleak] subread-2.0.3-source/src/index-builder.c:118:71: error: Memory leak: read_offsets [memleak] subread-2.0.3-source/src/index-builder.c:118:71: error: Memory leak: read_names [memleak] subread-2.0.3-source/src/index-builder.c:118:71: error: Memory leak: ginp [memleak] subread-2.0.3-source/src/index-builder.c:805:3: error: Memory leak: line_buf [memleak] subread-2.0.3-source/src/index-builder.c:805:3: error: Memory leak: read_head_buf [memleak] subread-2.0.3-source/src/index-builder.c:241:6: error: Common realloc mistake: 'read_offsets' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/index-builder.c:242:6: error: Common realloc mistake: 'read_names' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/index-builder.c:350:64: style: Same value in both branches of ternary operator. [duplicateValueTernary] subread-2.0.3-source/src/index-builder.c:363:95: style: Same value in both branches of ternary operator. [duplicateValueTernary] subread-2.0.3-source/src/index-builder.c:529:7: style: Local variable 'i' shadows outer variable [shadowVariable] subread-2.0.3-source/src/index-builder.c:474:19: note: Shadowed declaration subread-2.0.3-source/src/index-builder.c:529:7: note: Shadow variable subread-2.0.3-source/src/index-builder.c:946:10: style: Local variable 'line_buf_len' shadows outer variable [shadowVariable] subread-2.0.3-source/src/index-builder.c:845:8: note: Shadowed declaration subread-2.0.3-source/src/index-builder.c:946:10: note: Shadow variable subread-2.0.3-source/src/index-builder.c:56:47: style: Parameter 'bucket_sizes' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMhashtable.c:740:40: style:inconclusive: Function 'LRMisProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMhashtable.c:22:40: note: Function 'LRMisProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. subread-2.0.3-source/src/longread-one/LRMhashtable.c:740:40: note: Function 'LRMisProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:331:2: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/longread-one/LRMfile-io.c:337:2: warning: Return value of function deflate() is not used. [ignoredReturnValue] subread-2.0.3-source/src/longread-one/LRMfile-io.c:71:29: style:inconclusive: Function 'LRMreverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMfile-io.h:29:29: note: Function 'LRMreverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:71:29: note: Function 'LRMreverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:71:41: style:inconclusive: Function 'LRMreverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMfile-io.h:29:45: note: Function 'LRMreverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:71:41: note: Function 'LRMreverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:183:32: style:inconclusive: Function 'LRMreverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMfile-io.h:30:32: note: Function 'LRMreverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:183:32: note: Function 'LRMreverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:183:44: style:inconclusive: Function 'LRMreverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMfile-io.h:30:50: note: Function 'LRMreverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:183:44: note: Function 'LRMreverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:633:103: style:inconclusive: Function 'LRMlocate_chro_length' argument 4 names different: declaration 'chro_len' definition 'end_pos'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMfile-io.h:35:103: note: Function 'LRMlocate_chro_length' argument 4 names different: declaration 'chro_len' definition 'end_pos'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:633:103: note: Function 'LRMlocate_chro_length' argument 4 names different: declaration 'chro_len' definition 'end_pos'. subread-2.0.3-source/src/longread-one/LRMfile-io.c:506:7: style: Local variable 'new_need' shadows outer variable [shadowVariable] subread-2.0.3-source/src/longread-one/LRMfile-io.c:496:6: note: Shadowed declaration subread-2.0.3-source/src/longread-one/LRMfile-io.c:506:7: note: Shadow variable subread-2.0.3-source/src/longread-one/LRMfile-io.c:22:25: style: Parameter 'key' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMfile-io.c:203:89: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMfile-io.c:250:64: style: Parameter 'read' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMfile-io.c:250:77: style: Parameter 'qual' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMseek-zlib.c:193:31: style: Variable 'this_chunk_size' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/longread-one/LRMseek-zlib.c:273:20: style: Variable 'this_chunk_size' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/longread-one/LRMseek-zlib.c:277:50: style: Variable 'this_chunk_size' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:209:11: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:271:4: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:328:3: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:421:2: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:55:64: style:inconclusive: Function 'LRMgehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.h:31:64: note: Function 'LRMgehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:55:64: note: Function 'LRMgehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:443:176: style:inconclusive: Function 'LRMgehash_go_QQ' argument 5 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.h:44:176: note: Function 'LRMgehash_go_QQ' argument 5 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:443:176: note: Function 'LRMgehash_go_QQ' argument 5 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:202:68: style: Parameter 'src' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:427:24: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned] subread-2.0.3-source/src/longread-one/LRMsorted-hashtable.c:427:24: error: Signed integer overflow for expression '1<=(131-80)' is redundant or the array 'vtab->coverage_start[64973][51]' is accessed at index vtab->coverage_start[64973][51], which is out of bounds. [arrayIndexOutOfBoundsCond] subread-2.0.3-source/src/longread-one/longread-mapping.c:902:16: note: Assuming that condition 'test_ii>=(131-80)' is not redundant subread-2.0.3-source/src/longread-one/longread-mapping.c:898:42: note: Array index out of bounds subread-2.0.3-source/src/longread-one/longread-mapping.c:899:40: warning: Either the condition 'test_ii>=(131-80)' is redundant or the array 'vtab->coverage_end[64973][51]' is accessed at index vtab->coverage_end[64973][51], which is out of bounds. [arrayIndexOutOfBoundsCond] subread-2.0.3-source/src/longread-one/longread-mapping.c:902:16: note: Assuming that condition 'test_ii>=(131-80)' is not redundant subread-2.0.3-source/src/longread-one/longread-mapping.c:899:40: note: Array index out of bounds subread-2.0.3-source/src/longread-one/longread-mapping.c:978:64: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/longread-one/longread-mapping.c:899:18: style: Redundant initialization for 'this_read_end'. The initialized value is overwritten before it is read. [redundantInitialization] subread-2.0.3-source/src/longread-one/longread-mapping.c:858:22: note: this_read_end is initialized subread-2.0.3-source/src/longread-one/longread-mapping.c:899:18: note: this_read_end is overwritten subread-2.0.3-source/src/longread-one/longread-mapping.c:900:18: style: Redundant initialization for 'this_chro_pos'. The initialized value is overwritten before it is read. [redundantInitialization] subread-2.0.3-source/src/longread-one/longread-mapping.c:859:28: note: this_chro_pos is initialized subread-2.0.3-source/src/longread-one/longread-mapping.c:900:18: note: this_chro_pos is overwritten subread-2.0.3-source/src/longread-one/longread-mapping.c:977:33: style: Same value in both branches of ternary operator. [duplicateValueTernary] subread-2.0.3-source/src/longread-one/longread-mapping.c:1200:46: style: Parameter 'rname' can be declared with const [constParameter] subread-2.0.3-source/src/mergeVCF.c:285:6: error: Common realloc mistake: 'output_list' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/mergeVCF.c:27:27: style: Parameter 'ky' can be declared with const [constParameter] subread-2.0.3-source/src/qualityScores.c:164:12: style: Variable 'retstr' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/qualityScores.c:159:12: note: retstr is assigned subread-2.0.3-source/src/qualityScores.c:164:12: note: retstr is overwritten subread-2.0.3-source/src/qualityScores.c:164:12: style: Variable 'retstr' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/qualityScores.c:161:12: note: retstr is assigned subread-2.0.3-source/src/qualityScores.c:164:12: note: retstr is overwritten subread-2.0.3-source/src/qualityScores.c:100:60: style: Parameter 'qual_text' can be declared with const [constParameter] subread-2.0.3-source/src/qualityScores.c:348:29: style: Parameter 'input' can be declared with const [constParameter] subread-2.0.3-source/src/qualityScores.c:348:41: style: Parameter 'offset_pt' can be declared with const [constParameter] subread-2.0.3-source/src/qualityScores.c:348:63: style: Parameter 'size' can be declared with const [constParameter] subread-2.0.3-source/src/qualityScores.c:348:75: style: Parameter 'sam_whichend' can be declared with const [constParameter] subread-2.0.3-source/src/qualityScores.c:348:96: style: Parameter 'input_file_type' can be declared with const [constParameter] subread-2.0.3-source/src/qualityScores.c:348:121: style: Parameter 'output_sc' can be declared with const [constParameter] subread-2.0.3-source/src/removeDupReads.c:95:4: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/removeDupReads.c:56:3: error: Common realloc mistake: 'read_selection_list' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/sam2fq.c:63:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] subread-2.0.3-source/src/sam2fq.c:66:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] subread-2.0.3-source/src/longread-one/LRMchro-event.c:490:42: warning: Either the condition 'row_i>=0' is redundant or the array 'best_offset_history[2147483648]' is accessed at index -1, which is out of bounds. [negativeIndex] subread-2.0.3-source/src/longread-one/LRMchro-event.c:489:14: note: Assuming that condition 'row_i>=0' is not redundant subread-2.0.3-source/src/longread-one/LRMchro-event.c:490:42: note: Negative array index subread-2.0.3-source/src/longread-one/LRMchro-event.c:738:15: style: Condition 'read_i>=0' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/longread-one/LRMchro-event.c:705:15: note: Assuming that condition 'read_i>=0' is not redundant subread-2.0.3-source/src/longread-one/LRMchro-event.c:723:56: note: Assuming condition is false subread-2.0.3-source/src/longread-one/LRMchro-event.c:738:15: note: Condition 'read_i>=0' is always true subread-2.0.3-source/src/longread-one/LRMchro-event.c:745:15: style: Condition 'read_i>=0' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/longread-one/LRMchro-event.c:705:15: note: Assuming that condition 'read_i>=0' is not redundant subread-2.0.3-source/src/longread-one/LRMchro-event.c:723:56: note: Assuming condition is false subread-2.0.3-source/src/longread-one/LRMchro-event.c:745:15: note: Condition 'read_i>=0' is always true subread-2.0.3-source/src/longread-one/LRMchro-event.c:114:5: error: Common realloc mistake: 'entries_list' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/longread-one/LRMchro-event.c:143:5: error: Common realloc mistake: 'new_space' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/longread-one/LRMchro-event.c:95:5: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck] subread-2.0.3-source/src/longread-one/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant subread-2.0.3-source/src/longread-one/LRMchro-event.c:95:5: note: Null pointer dereference subread-2.0.3-source/src/longread-one/LRMchro-event.c:96:5: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck] subread-2.0.3-source/src/longread-one/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant subread-2.0.3-source/src/longread-one/LRMchro-event.c:96:5: note: Null pointer dereference subread-2.0.3-source/src/longread-one/LRMchro-event.c:100:21: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck] subread-2.0.3-source/src/longread-one/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant subread-2.0.3-source/src/longread-one/LRMchro-event.c:100:21: note: Null pointer dereference subread-2.0.3-source/src/longread-one/LRMchro-event.c:104:13: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck] subread-2.0.3-source/src/longread-one/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant subread-2.0.3-source/src/longread-one/LRMchro-event.c:104:13: note: Null pointer dereference subread-2.0.3-source/src/longread-one/LRMchro-event.c:640:108: style: Same expression on both sides of '&&'. [duplicateExpression] subread-2.0.3-source/src/longread-one/LRMchro-event.c:358:2: style: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode] subread-2.0.3-source/src/longread-one/LRMchro-event.c:22:28: style: Parameter 'ch1' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMchro-event.c:22:40: style: Parameter 'ch2' can be declared with const [constParameter] subread-2.0.3-source/src/longread-one/LRMchro-event.c:127:64: style: Parameter 'order_index' can be declared with const [constParameter] subread-2.0.3-source/src/sambam-file.c:1219:2: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/sambam-file.c:1225:2: warning: Return value of function deflate() is not used. [ignoredReturnValue] subread-2.0.3-source/src/sambam-file.c:2394:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/sambam-file.c:1014:7: style: Condition 'bam_is_broken' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/sambam-file.c:1006:127: note: Assignment 'bam_is_broken=0', assigned value is 0 subread-2.0.3-source/src/sambam-file.c:1014:7: note: Condition 'bam_is_broken' is always false subread-2.0.3-source/src/sambam-file.c:92:15: error: Resource leak: fp [resourceLeak] subread-2.0.3-source/src/sambam-file.c:1047:7: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/sambam-file.c:1041:7: note: ret is assigned subread-2.0.3-source/src/sambam-file.c:1047:7: note: ret is overwritten subread-2.0.3-source/src/sambam-file.c:2028:8: style: Variable 'rlen' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/sambam-file.c:2027:8: note: rlen is assigned subread-2.0.3-source/src/sambam-file.c:2028:8: note: rlen is overwritten subread-2.0.3-source/src/seek-zlib.c:663:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/seek-zlib.c:484:7: style: Condition 'buff' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/seek-zlib.c:480:6: note: Assuming that condition 'buff' is not redundant subread-2.0.3-source/src/seek-zlib.c:484:7: note: Condition 'buff' is always true subread-2.0.3-source/src/seek-zlib.c:228:5: error: Common realloc mistake: 'arr' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/seek-zlib.c:307:5: error: Common realloc mistake: 'out_txt' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/sambam-file.c:2243:33: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS] subread-2.0.3-source/src/sambam-file.c:1001:78: style:inconclusive: Function 'PBum_load_header' argument 3 names different: declaration 'remainder_read_data' definition 'remainder_reads_data'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:160:78: note: Function 'PBum_load_header' argument 3 names different: declaration 'remainder_read_data' definition 'remainder_reads_data'. subread-2.0.3-source/src/sambam-file.c:1001:78: note: Function 'PBum_load_header' argument 3 names different: declaration 'remainder_read_data' definition 'remainder_reads_data'. subread-2.0.3-source/src/seek-zlib.c:439:47: style:inconclusive: Function 'seekgz_gets' argument 2 names different: declaration 'buf' definition 'buff'. [funcArgNamesDifferent] subread-2.0.3-source/src/seek-zlib.h:48:47: note: Function 'seekgz_gets' argument 2 names different: declaration 'buf' definition 'buff'. subread-2.0.3-source/src/seek-zlib.c:439:47: note: Function 'seekgz_gets' argument 2 names different: declaration 'buf' definition 'buff'. subread-2.0.3-source/src/sambam-file.c:1001:107: style:inconclusive: Function 'PBum_load_header' argument 4 names different: declaration 'remainder_read_data_len' definition 'remainder_reads_data_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:160:105: note: Function 'PBum_load_header' argument 4 names different: declaration 'remainder_read_data_len' definition 'remainder_reads_data_len'. subread-2.0.3-source/src/sambam-file.c:1001:107: note: Function 'PBum_load_header' argument 4 names different: declaration 'remainder_read_data_len' definition 'remainder_reads_data_len'. subread-2.0.3-source/src/seek-zlib.c:439:57: style:inconclusive: Function 'seekgz_gets' argument 3 names different: declaration 'buf_size' definition 'buff_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/seek-zlib.h:48:56: note: Function 'seekgz_gets' argument 3 names different: declaration 'buf_size' definition 'buff_len'. subread-2.0.3-source/src/seek-zlib.c:439:57: note: Function 'seekgz_gets' argument 3 names different: declaration 'buf_size' definition 'buff_len'. subread-2.0.3-source/src/sambam-file.c:1097:110: style:inconclusive: Function 'SamBam_writer_create' argument 5 names different: declaration 'is_tmp_BAM' definition 'is_temp_BAM_file'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:197:110: note: Function 'SamBam_writer_create' argument 5 names different: declaration 'is_tmp_BAM' definition 'is_temp_BAM_file'. subread-2.0.3-source/src/sambam-file.c:1097:110: note: Function 'SamBam_writer_create' argument 5 names different: declaration 'is_tmp_BAM' definition 'is_temp_BAM_file'. subread-2.0.3-source/src/seek-zlib.c:678:81: style:inconclusive: Function 'parallel_gzip_zip_texts' argument 3 names different: declaration 'for_eof_marker' definition 'eof_marker'. [funcArgNamesDifferent] subread-2.0.3-source/src/seek-zlib.h:39:81: note: Function 'parallel_gzip_zip_texts' argument 3 names different: declaration 'for_eof_marker' definition 'eof_marker'. subread-2.0.3-source/src/seek-zlib.c:678:81: note: Function 'parallel_gzip_zip_texts' argument 3 names different: declaration 'for_eof_marker' definition 'eof_marker'. subread-2.0.3-source/src/sambam-file.c:1401:106: style:inconclusive: Function 'SamBam_writer_add_chromosome' argument 4 names different: declaration 'add_header_too' definition 'add_header'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:203:106: note: Function 'SamBam_writer_add_chromosome' argument 4 names different: declaration 'add_header_too' definition 'add_header'. subread-2.0.3-source/src/sambam-file.c:1401:106: note: Function 'SamBam_writer_add_chromosome' argument 4 names different: declaration 'add_header_too' definition 'add_header'. subread-2.0.3-source/src/sambam-file.c:1607:53: style:inconclusive: Function 'duplicate_TAB_record_field' argument 2 names different: declaration 'fld_no' definition 'fno'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:231:52: note: Function 'duplicate_TAB_record_field' argument 2 names different: declaration 'fld_no' definition 'fno'. subread-2.0.3-source/src/sambam-file.c:1607:53: note: Function 'duplicate_TAB_record_field' argument 2 names different: declaration 'fld_no' definition 'fno'. subread-2.0.3-source/src/sambam-file.c:1607:62: style:inconclusive: Function 'duplicate_TAB_record_field' argument 3 names different: declaration 'toend' definition 'to_end'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:231:64: note: Function 'duplicate_TAB_record_field' argument 3 names different: declaration 'toend' definition 'to_end'. subread-2.0.3-source/src/sambam-file.c:1607:62: note: Function 'duplicate_TAB_record_field' argument 3 names different: declaration 'toend' definition 'to_end'. subread-2.0.3-source/src/sambam-file.c:1668:90: style:inconclusive: Function 'SamBam_writer_add_read_line' argument 4 names different: declaration 'commitable' definition 'committable'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:230:90: note: Function 'SamBam_writer_add_read_line' argument 4 names different: declaration 'commitable' definition 'committable'. subread-2.0.3-source/src/sambam-file.c:1668:90: note: Function 'SamBam_writer_add_read_line' argument 4 names different: declaration 'commitable' definition 'committable'. subread-2.0.3-source/src/sambam-file.c:1704:56: style:inconclusive: Function 'SamBam_writer_add_read' argument 2 names different: declaration 'threadno' definition 'thread_no'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:211:56: note: Function 'SamBam_writer_add_read' argument 2 names different: declaration 'threadno' definition 'thread_no'. subread-2.0.3-source/src/sambam-file.c:1704:56: note: Function 'SamBam_writer_add_read' argument 2 names different: declaration 'threadno' definition 'thread_no'. subread-2.0.3-source/src/sambam-file.c:1704:222: style:inconclusive: Function 'SamBam_writer_add_read' argument 10 names different: declaration 'next_chro_pos' definition 'next_chro_position'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:211:221: note: Function 'SamBam_writer_add_read' argument 10 names different: declaration 'next_chro_pos' definition 'next_chro_position'. subread-2.0.3-source/src/sambam-file.c:1704:222: note: Function 'SamBam_writer_add_read' argument 10 names different: declaration 'next_chro_pos' definition 'next_chro_position'. subread-2.0.3-source/src/sambam-file.c:1704:337: style:inconclusive: Function 'SamBam_writer_add_read' argument 16 names different: declaration 'can_submit' definition 'committable'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:211:331: note: Function 'SamBam_writer_add_read' argument 16 names different: declaration 'can_submit' definition 'committable'. subread-2.0.3-source/src/sambam-file.c:1704:337: note: Function 'SamBam_writer_add_read' argument 16 names different: declaration 'can_submit' definition 'committable'. subread-2.0.3-source/src/sambam-file.c:1799:34: style:inconclusive: Function 'SamBam_unzip' argument 2 names different: declaration 'out_max_len' definition 'outlen'. [funcArgNamesDifferent] subread-2.0.3-source/src/sambam-file.h:217:34: note: Function 'SamBam_unzip' argument 2 names different: declaration 'out_max_len' definition 'outlen'. subread-2.0.3-source/src/sambam-file.c:1799:34: note: Function 'SamBam_unzip' argument 2 names different: declaration 'out_max_len' definition 'outlen'. subread-2.0.3-source/src/seek-zlib.c:756:69: style: Parameter 'outfps' can be declared with const [constParameter] subread-2.0.3-source/src/sambam-file.c:1426:34: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/sambam-file.c:1460:29: style: Parameter 'read_txt' can be declared with const [constParameter] subread-2.0.3-source/src/sambam-file.c:1789:56: error: Uninitialized variable: additional_bin [uninitvar] subread-2.0.3-source/src/sambam-file.c:126:23: style: Variable 'nchold' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/sambam-file.c:1006:125: style: Variable 'bam_is_broken' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/sambam-file.c:1898:25: style: Variable 'ret' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/sambam-file.c:2028:8: style: Variable 'rlen' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/sublog.c:87:5: style: Condition 'to_remove_ESC' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/sublog.c:80:22: note: Assignment 'to_remove_ESC=1', assigned value is 1 subread-2.0.3-source/src/sublog.c:87:5: note: Condition 'to_remove_ESC' is always true subread-2.0.3-source/src/sublog.c:122:5: style: Condition 'to_remove_ESC' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/sublog.c:117:22: note: Assignment 'to_remove_ESC=1', assigned value is 1 subread-2.0.3-source/src/sublog.c:122:5: note: Condition 'to_remove_ESC' is always true subread-2.0.3-source/src/sublog.c:78:36: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing] subread-2.0.3-source/src/sublog.c:115:36: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing] subread-2.0.3-source/src/subtools.c:208:21: style: Condition '!out_SAM' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/subtools.c:184:6: note: Assuming that condition 'out_SAM' is not redundant subread-2.0.3-source/src/subtools.c:208:21: note: Condition '!out_SAM' is always true subread-2.0.3-source/src/subtools.c:148:8: style: Local variable 'ret' shadows outer variable [shadowVariable] subread-2.0.3-source/src/subtools.c:135:7: note: Shadowed declaration subread-2.0.3-source/src/subtools.c:148:8: note: Shadow variable subread-2.0.3-source/src/subtools.c:173:10: style: Variable 'in_SAM' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/test-seek-zlib.c:92:4: warning: %lld in format string (no. 3) requires 'long long' but the argument type is 'unsigned long long'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/test-seek-zlib.c:17:33: style: Variable 'marked' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/test_qs.c:32:2: error: Found a exit path from function with non-void return type that has missing return statement [missingReturn] subread-2.0.3-source/src/test_qs.c:15:5: style: Variable 'val' can be declared with const [constVariable] subread-2.0.3-source/src/tx-unique.c:365:10: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck] subread-2.0.3-source/src/tx-unique.c:366:5: note: Assuming that condition '!out_fp' is not redundant subread-2.0.3-source/src/tx-unique.c:365:10: note: Null pointer dereference subread-2.0.3-source/src/tx-unique.c:126:22: style: Local variable 'memex' shadows outer variable [shadowVariable] subread-2.0.3-source/src/tx-unique.c:118:20: note: Shadowed declaration subread-2.0.3-source/src/tx-unique.c:126:22: note: Shadow variable subread-2.0.3-source/src/sorted-hashtable.c:881:32: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][21], which is out of bounds. [arrayIndexOutOfBoundsCond] subread-2.0.3-source/src/sorted-hashtable.c:877:18: note: Assuming that condition 'toli<7*3' is not redundant subread-2.0.3-source/src/sorted-hashtable.c:881:32: note: Array index out of bounds subread-2.0.3-source/src/sorted-hashtable.c:882:32: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][22], which is out of bounds. [arrayIndexOutOfBoundsCond] subread-2.0.3-source/src/sorted-hashtable.c:877:18: note: Assuming that condition 'toli<7*3' is not redundant subread-2.0.3-source/src/sorted-hashtable.c:882:32: note: Array index out of bounds subread-2.0.3-source/src/sorted-hashtable.c:1057:31: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][21], which is out of bounds. [arrayIndexOutOfBoundsCond] subread-2.0.3-source/src/sorted-hashtable.c:1053:17: note: Assuming that condition 'toli<7*3' is not redundant subread-2.0.3-source/src/sorted-hashtable.c:1057:31: note: Array index out of bounds subread-2.0.3-source/src/sorted-hashtable.c:1058:31: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][22], which is out of bounds. [arrayIndexOutOfBoundsCond] subread-2.0.3-source/src/sorted-hashtable.c:1053:17: note: Assuming that condition 'toli<7*3' is not redundant subread-2.0.3-source/src/sorted-hashtable.c:1058:31: note: Array index out of bounds subread-2.0.3-source/src/sorted-hashtable.c:1151:11: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] subread-2.0.3-source/src/sorted-hashtable.c:142:4: error: Memory leak: new_item_values [memleak] subread-2.0.3-source/src/sorted-hashtable.c:1484:4: error: Memory leak: bucket_bytes [memleak] subread-2.0.3-source/src/sorted-hashtable.c:180:38: style: Same expression on both sides of '||'. [duplicateExpression] subread-2.0.3-source/src/sorted-hashtable.c:42:48: style:inconclusive: Function 'calculate_buckets_by_size' argument 1 names different: declaration 'exp_size' definition 'expected_size'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:101:47: note: Function 'calculate_buckets_by_size' argument 1 names different: declaration 'exp_size' definition 'expected_size'. subread-2.0.3-source/src/sorted-hashtable.c:42:48: note: Function 'calculate_buckets_by_size' argument 1 names different: declaration 'exp_size' definition 'expected_size'. subread-2.0.3-source/src/sorted-hashtable.c:42:67: style:inconclusive: Function 'calculate_buckets_by_size' argument 2 names different: declaration 'version' definition 'version_number'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:101:61: note: Function 'calculate_buckets_by_size' argument 2 names different: declaration 'version' definition 'version_number'. subread-2.0.3-source/src/sorted-hashtable.c:42:67: note: Function 'calculate_buckets_by_size' argument 2 names different: declaration 'version' definition 'version_number'. subread-2.0.3-source/src/sorted-hashtable.c:42:87: style:inconclusive: Function 'calculate_buckets_by_size' argument 3 names different: declaration 'is_small_tab' definition 'is_small_table'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:101:74: note: Function 'calculate_buckets_by_size' argument 3 names different: declaration 'is_small_tab' definition 'is_small_table'. subread-2.0.3-source/src/sorted-hashtable.c:42:87: note: Function 'calculate_buckets_by_size' argument 3 names different: declaration 'is_small_tab' definition 'is_small_table'. subread-2.0.3-source/src/sorted-hashtable.c:77:111: style:inconclusive: Function 'gehash_create_ex' argument 5 names different: declaration 'GENE_SLIDING_STEP' definition 'index_gap'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:42:111: note: Function 'gehash_create_ex' argument 5 names different: declaration 'GENE_SLIDING_STEP' definition 'index_gap'. subread-2.0.3-source/src/sorted-hashtable.c:77:111: note: Function 'gehash_create_ex' argument 5 names different: declaration 'GENE_SLIDING_STEP' definition 'index_gap'. subread-2.0.3-source/src/sorted-hashtable.c:305:91: style:inconclusive: Function 'gehash_insert_limited' argument 4 names different: declaration 'max_key_occurance' definition 'limit'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:49:91: note: Function 'gehash_insert_limited' argument 4 names different: declaration 'max_key_occurance' definition 'limit'. subread-2.0.3-source/src/sorted-hashtable.c:305:91: note: Function 'gehash_insert_limited' argument 4 names different: declaration 'max_key_occurance' definition 'limit'. subread-2.0.3-source/src/sorted-hashtable.c:305:102: style:inconclusive: Function 'gehash_insert_limited' argument 5 names different: declaration 'prob_replace' definition 'replace_prob'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:49:114: note: Function 'gehash_insert_limited' argument 5 names different: declaration 'prob_replace' definition 'replace_prob'. subread-2.0.3-source/src/sorted-hashtable.c:305:102: note: Function 'gehash_insert_limited' argument 5 names different: declaration 'prob_replace' definition 'replace_prob'. subread-2.0.3-source/src/sorted-hashtable.c:515:55: style:inconclusive: Function 'gehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:65:55: note: Function 'gehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/sorted-hashtable.c:515:55: note: Function 'gehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/sorted-hashtable.c:937:55: style:inconclusive: Function 'gehash_go_X' argument 2 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:66:55: note: Function 'gehash_go_X' argument 2 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/sorted-hashtable.c:937:55: note: Function 'gehash_go_X' argument 2 names different: declaration 'key' definition 'raw_key'. subread-2.0.3-source/src/sorted-hashtable.c:937:249: style:inconclusive: Function 'gehash_go_X' argument 12 names different: declaration 'shift_indel_locations' definition 'shift_indel_locs'. [funcArgNamesDifferent] subread-2.0.3-source/src/sorted-hashtable.h:66:244: note: Function 'gehash_go_X' argument 12 names different: declaration 'shift_indel_locations' definition 'shift_indel_locs'. subread-2.0.3-source/src/sorted-hashtable.c:937:249: note: Function 'gehash_go_X' argument 12 names different: declaration 'shift_indel_locations' definition 'shift_indel_locs'. subread-2.0.3-source/src/sorted-hashtable.c:200:94: style: Parameter 'bucket_sizes' can be declared with const [constParameter] subread-2.0.3-source/src/sorted-hashtable.c:1144:73: style: Parameter 'src' can be declared with const [constParameter] subread-2.0.3-source/src/sorted-hashtable.c:203:15: style: Variable 'is_fault' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:5322:2: error: Address of local auto-variable assigned to a function parameter. [autoVariables] subread-2.0.3-source/src/input-files.c:5323:2: error: Address of local auto-variable assigned to a function parameter. [autoVariables] subread-2.0.3-source/src/input-files.c:2202:19: error: Array 'this_gene_name[128]' accessed at index 1199, which is out of bounds. [arrayIndexOutOfBounds] subread-2.0.3-source/src/input-files.c:2203:18: error: Array 'this_gene_name[128]' accessed at index 1200, which is out of bounds. [arrayIndexOutOfBounds] subread-2.0.3-source/src/input-files.c:2201:4: note: After for loop, i has value 1200 subread-2.0.3-source/src/input-files.c:2203:18: note: Array index out of bounds subread-2.0.3-source/src/input-files.c:2255:3: warning:inconclusive: The buffer 'old_gene_name' may not be null-terminated after the call to strncpy(). [terminateStrncpy] subread-2.0.3-source/src/input-files.c:2386:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:2448:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:2614:3: warning: Return value of function inflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:4795:4: warning: Return value of function deflate() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:4809:4: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:4816:4: warning: Return value of function deflate() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:4889:2: warning: Return value of function inflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:4897:2: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:5573:2: warning: Return value of function inflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/input-files.c:67:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/input-files.c:2332:19: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled] subread-2.0.3-source/src/input-files.c:4576:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/input-files.c:5247:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/input-files.c:5406:19: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/input-files.c:5537:19: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] subread-2.0.3-source/src/input-files.c:5918:6: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] subread-2.0.3-source/src/input-files.c:6069:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled] subread-2.0.3-source/src/input-files.c:5587:18: style: Condition 'disk_is_full' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/input-files.c:5578:22: note: Assignment 'disk_is_full=0', assigned value is 0 subread-2.0.3-source/src/input-files.c:5587:18: note: Condition 'disk_is_full' is always false subread-2.0.3-source/src/input-files.c:1506:2: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/input-files.c:3001:7: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long long'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/input-files.c:3558:21: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/input-files.c:3558:21: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/input-files.c:4541:5: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long long'. [invalidPrintfArgType_uint] subread-2.0.3-source/src/input-files.c:5984:7: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/input-files.c:6074:7: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/input-files.c:6240:4: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/input-files.c:2952:7: error: Common realloc mistake: 'header_txt' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:4196:5: error: Common realloc mistake: 'orphant_fps' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:4279:6: error: Common realloc mistake: 'orphant_fps' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:5604:4: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:5624:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:5631:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:5649:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:5657:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/input-files.c:3047:38: warning: Either the condition 'NULL==line_ptr' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck] subread-2.0.3-source/src/input-files.c:3046:13: note: Assuming that condition 'NULL==line_ptr' is not redundant subread-2.0.3-source/src/input-files.c:3047:38: note: Null pointer subtraction subread-2.0.3-source/src/input-files.c:4734:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/input-files.c:4733:6: note: x1 is assigned subread-2.0.3-source/src/input-files.c:4734:6: note: x1 is overwritten subread-2.0.3-source/src/input-files.c:4735:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/input-files.c:4734:6: note: x1 is assigned subread-2.0.3-source/src/input-files.c:4735:6: note: x1 is overwritten subread-2.0.3-source/src/input-files.c:4736:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/input-files.c:4735:6: note: x1 is assigned subread-2.0.3-source/src/input-files.c:4736:6: note: x1 is overwritten subread-2.0.3-source/src/input-files.c:4738:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/input-files.c:4736:6: note: x1 is assigned subread-2.0.3-source/src/input-files.c:4738:6: note: x1 is overwritten subread-2.0.3-source/src/input-files.c:4740:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/input-files.c:4738:6: note: x1 is assigned subread-2.0.3-source/src/input-files.c:4740:6: note: x1 is overwritten subread-2.0.3-source/src/input-files.c:5587:42: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary] subread-2.0.3-source/src/input-files.c:3995:50: warning: Either the condition 'all_threads<0' is redundant or there is division by zero at line 3995. [zerodivcond] subread-2.0.3-source/src/input-files.c:3995:18: note: Assuming that condition 'all_threads<0' is not redundant subread-2.0.3-source/src/input-files.c:3995:50: note: Division by zero subread-2.0.3-source/src/input-files.c:104:67: style:inconclusive: Function 'guess_reads_density_format' argument 3 names different: declaration 'min_phred' definition 'min_phred_score'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:279:67: note: Function 'guess_reads_density_format' argument 3 names different: declaration 'min_phred' definition 'min_phred_score'. subread-2.0.3-source/src/input-files.c:104:67: note: Function 'guess_reads_density_format' argument 3 names different: declaration 'min_phred' definition 'min_phred_score'. subread-2.0.3-source/src/input-files.c:104:90: style:inconclusive: Function 'guess_reads_density_format' argument 4 names different: declaration 'max_phred' definition 'max_phred_score'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:279:84: note: Function 'guess_reads_density_format' argument 4 names different: declaration 'max_phred' definition 'max_phred_score'. subread-2.0.3-source/src/input-files.c:104:90: note: Function 'guess_reads_density_format' argument 4 names different: declaration 'max_phred' definition 'max_phred_score'. subread-2.0.3-source/src/input-files.c:265:19: style:inconclusive: Function 'read_line' argument 1 names different: declaration 'max_len' definition 'max_read_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:245:19: note: Function 'read_line' argument 1 names different: declaration 'max_len' definition 'max_read_len'. subread-2.0.3-source/src/input-files.c:265:19: note: Function 'read_line' argument 1 names different: declaration 'max_len' definition 'max_read_len'. subread-2.0.3-source/src/input-files.c:265:61: style:inconclusive: Function 'read_line' argument 4 names different: declaration 'conv_to_upper' definition 'must_upper'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:245:56: note: Function 'read_line' argument 4 names different: declaration 'conv_to_upper' definition 'must_upper'. subread-2.0.3-source/src/input-files.c:265:61: note: Function 'read_line' argument 4 names different: declaration 'conv_to_upper' definition 'must_upper'. subread-2.0.3-source/src/input-files.c:346:51: style:inconclusive: Function 'geinput_readline' argument 2 names different: declaration 'linebuffer' definition 'buff'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:238:51: note: Function 'geinput_readline' argument 2 names different: declaration 'linebuffer' definition 'buff'. subread-2.0.3-source/src/input-files.c:346:51: note: Function 'geinput_readline' argument 2 names different: declaration 'linebuffer' definition 'buff'. subread-2.0.3-source/src/input-files.c:390:35: style:inconclusive: Function 'geinput_open_scRNA_BAM' argument 1 names different: declaration 'fnames' definition 'rfnames'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:335:35: note: Function 'geinput_open_scRNA_BAM' argument 1 names different: declaration 'fnames' definition 'rfnames'. subread-2.0.3-source/src/input-files.c:390:35: note: Function 'geinput_open_scRNA_BAM' argument 1 names different: declaration 'fnames' definition 'rfnames'. subread-2.0.3-source/src/input-files.c:398:35: style:inconclusive: Function 'geinput_open_scRNA_fqs' argument 1 names different: declaration 'fnames' definition 'rfnames'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:334:35: note: Function 'geinput_open_scRNA_fqs' argument 1 names different: declaration 'fnames' definition 'rfnames'. subread-2.0.3-source/src/input-files.c:398:35: note: Function 'geinput_open_scRNA_fqs' argument 1 names different: declaration 'fnames' definition 'rfnames'. subread-2.0.3-source/src/input-files.c:406:73: style:inconclusive: Function 'geinput_open_bcl' argument 3 names different: declaration 'reads_in_chunk' definition 'reads_per_chunk'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:336:73: note: Function 'geinput_open_bcl' argument 3 names different: declaration 'reads_in_chunk' definition 'reads_per_chunk'. subread-2.0.3-source/src/input-files.c:406:73: note: Function 'geinput_open_bcl' argument 3 names different: declaration 'reads_in_chunk' definition 'reads_per_chunk'. subread-2.0.3-source/src/input-files.c:415:71: style:inconclusive: Function 'geinput_open_sam' argument 3 names different: declaration 'half_no' definition 'half_number'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:216:71: note: Function 'geinput_open_sam' argument 3 names different: declaration 'half_no' definition 'half_number'. subread-2.0.3-source/src/input-files.c:415:71: note: Function 'geinput_open_sam' argument 3 names different: declaration 'half_no' definition 'half_number'. subread-2.0.3-source/src/input-files.c:641:56: style:inconclusive: Function 'geinput_readline_back' argument 2 names different: declaration 'linebuffer' definition 'linebuffer_3000'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:219:56: note: Function 'geinput_readline_back' argument 2 names different: declaration 'linebuffer' definition 'linebuffer_3000'. subread-2.0.3-source/src/input-files.c:641:56: note: Function 'geinput_readline_back' argument 2 names different: declaration 'linebuffer' definition 'linebuffer_3000'. subread-2.0.3-source/src/input-files.c:1094:26: style:inconclusive: Function 'reverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:255:26: note: Function 'reverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. subread-2.0.3-source/src/input-files.c:1094:26: note: Function 'reverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. subread-2.0.3-source/src/input-files.c:1094:38: style:inconclusive: Function 'reverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:255:42: note: Function 'reverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/input-files.c:1094:38: note: Function 'reverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/input-files.c:1173:29: style:inconclusive: Function 'reverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:257:29: note: Function 'reverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. subread-2.0.3-source/src/input-files.c:1173:29: note: Function 'reverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. subread-2.0.3-source/src/input-files.c:1173:41: style:inconclusive: Function 'reverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:257:47: note: Function 'reverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/input-files.c:1173:41: note: Function 'reverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. subread-2.0.3-source/src/input-files.c:1557:312: style:inconclusive: Function 'write_read_block_file' argument 16 names different: declaration 'M_seg' definition 'mapped_seg'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:283:312: note: Function 'write_read_block_file' argument 16 names different: declaration 'M_seg' definition 'mapped_seg'. subread-2.0.3-source/src/input-files.c:1557:312: note: Function 'write_read_block_file' argument 16 names different: declaration 'M_seg' definition 'mapped_seg'. subread-2.0.3-source/src/input-files.c:1835:44: style:inconclusive: Function 'break_SAM_file' argument 2 names different: declaration 'is_BAM' definition 'is_BAM_file'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:268:44: note: Function 'break_SAM_file' argument 2 names different: declaration 'is_BAM' definition 'is_BAM_file'. subread-2.0.3-source/src/input-files.c:1835:44: note: Function 'break_SAM_file' argument 2 names different: declaration 'is_BAM' definition 'is_BAM_file'. subread-2.0.3-source/src/input-files.c:1835:120: style:inconclusive: Function 'break_SAM_file' argument 5 names different: declaration 'block_no' definition 'block_count'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:268:115: note: Function 'break_SAM_file' argument 5 names different: declaration 'block_no' definition 'block_count'. subread-2.0.3-source/src/input-files.c:1835:120: note: Function 'break_SAM_file' argument 5 names different: declaration 'block_no' definition 'block_count'. subread-2.0.3-source/src/input-files.c:1835:288: style:inconclusive: Function 'break_SAM_file' argument 11 names different: declaration 'all_Mapped_bases' definition 'all_mapped_bases'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:268:280: note: Function 'break_SAM_file' argument 11 names different: declaration 'all_Mapped_bases' definition 'all_mapped_bases'. subread-2.0.3-source/src/input-files.c:1835:288: note: Function 'break_SAM_file' argument 11 names different: declaration 'all_Mapped_bases' definition 'all_mapped_bases'. subread-2.0.3-source/src/input-files.c:1835:318: style:inconclusive: Function 'break_SAM_file' argument 12 names different: declaration 'event_table_ptr' definition 'event_table'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:268:311: note: Function 'break_SAM_file' argument 12 names different: declaration 'event_table_ptr' definition 'event_table'. subread-2.0.3-source/src/input-files.c:1835:318: note: Function 'break_SAM_file' argument 12 names different: declaration 'event_table_ptr' definition 'event_table'. subread-2.0.3-source/src/input-files.c:1835:431: style:inconclusive: Function 'break_SAM_file' argument 17 names different: declaration 'use_soft_clipped_bases' definition 'use_softclipped_bases'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:268:428: note: Function 'break_SAM_file' argument 17 names different: declaration 'use_soft_clipped_bases' definition 'use_softclipped_bases'. subread-2.0.3-source/src/input-files.c:1835:431: note: Function 'break_SAM_file' argument 17 names different: declaration 'use_soft_clipped_bases' definition 'use_softclipped_bases'. subread-2.0.3-source/src/input-files.c:2261:28: style:inconclusive: Function 'does_file_exist' argument 1 names different: declaration 'filename' definition 'path'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:277:29: note: Function 'does_file_exist' argument 1 names different: declaration 'filename' definition 'path'. subread-2.0.3-source/src/input-files.c:2261:28: note: Function 'does_file_exist' argument 1 names different: declaration 'filename' definition 'path'. subread-2.0.3-source/src/input-files.c:2365:106: style:inconclusive: Function 'SAM_pairer_writer_create' argument 4 names different: declaration 'BAM_output' definition 'BAM_input'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:324:106: note: Function 'SAM_pairer_writer_create' argument 4 names different: declaration 'BAM_output' definition 'BAM_input'. subread-2.0.3-source/src/input-files.c:2365:106: note: Function 'SAM_pairer_writer_create' argument 4 names different: declaration 'BAM_output' definition 'BAM_input'. subread-2.0.3-source/src/input-files.c:2365:121: style:inconclusive: Function 'SAM_pairer_writer_create' argument 5 names different: declaration 'BAM_compression_level' definition 'c_level'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:324:122: note: Function 'SAM_pairer_writer_create' argument 5 names different: declaration 'BAM_compression_level' definition 'c_level'. subread-2.0.3-source/src/input-files.c:2365:121: note: Function 'SAM_pairer_writer_create' argument 5 names different: declaration 'BAM_compression_level' definition 'c_level'. subread-2.0.3-source/src/input-files.c:3420:40: style:inconclusive: Function 'SAP_pairer_skip_tag_body_len' argument 1 names different: declaration 'tag_start' definition 'bin'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:323:41: note: Function 'SAP_pairer_skip_tag_body_len' argument 1 names different: declaration 'tag_start' definition 'bin'. subread-2.0.3-source/src/input-files.c:3420:40: note: Function 'SAP_pairer_skip_tag_body_len' argument 1 names different: declaration 'tag_start' definition 'bin'. subread-2.0.3-source/src/input-files.c:3593:41: style:inconclusive: Function 'SAM_pairer_get_tag_bin_start' argument 1 names different: declaration 'bin' definition 'bin1'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:329:41: note: Function 'SAM_pairer_get_tag_bin_start' argument 1 names different: declaration 'bin' definition 'bin1'. subread-2.0.3-source/src/input-files.c:3593:41: note: Function 'SAM_pairer_get_tag_bin_start' argument 1 names different: declaration 'bin' definition 'bin1'. subread-2.0.3-source/src/input-files.c:3769:38: style:inconclusive: Function 'SAM_pairer_writer_reset' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:318:37: note: Function 'SAM_pairer_writer_reset' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. subread-2.0.3-source/src/input-files.c:3769:38: note: Function 'SAM_pairer_writer_reset' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. subread-2.0.3-source/src/input-files.c:3786:43: style:inconclusive: Function 'SAM_pairer_multi_thread_output' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:321:44: note: Function 'SAM_pairer_multi_thread_output' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. subread-2.0.3-source/src/input-files.c:3786:43: note: Function 'SAM_pairer_multi_thread_output' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. subread-2.0.3-source/src/input-files.c:6321:47: style:inconclusive: Function 'is_certainly_bam_file' argument 2 names different: declaration 'is_firstread_PE' definition 'is_first_read_PE'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:300:47: note: Function 'is_certainly_bam_file' argument 2 names different: declaration 'is_firstread_PE' definition 'is_first_read_PE'. subread-2.0.3-source/src/input-files.c:6321:47: note: Function 'is_certainly_bam_file' argument 2 names different: declaration 'is_firstread_PE' definition 'is_first_read_PE'. subread-2.0.3-source/src/input-files.c:6321:76: style:inconclusive: Function 'is_certainly_bam_file' argument 3 names different: declaration 'SAMBAM_header_length' definition 'SAMBAM_header_size'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:300:76: note: Function 'is_certainly_bam_file' argument 3 names different: declaration 'SAMBAM_header_length' definition 'SAMBAM_header_size'. subread-2.0.3-source/src/input-files.c:6321:76: note: Function 'is_certainly_bam_file' argument 3 names different: declaration 'SAMBAM_header_length' definition 'SAMBAM_header_size'. subread-2.0.3-source/src/input-files.c:6549:41: style:inconclusive: Function 'probe_file_type' argument 2 names different: declaration 'is_first_PE' definition 'is_first_read_PE'. [funcArgNamesDifferent] subread-2.0.3-source/src/input-files.h:307:41: note: Function 'probe_file_type' argument 2 names different: declaration 'is_first_PE' definition 'is_first_read_PE'. subread-2.0.3-source/src/input-files.c:6549:41: note: Function 'probe_file_type' argument 2 names different: declaration 'is_first_PE' definition 'is_first_read_PE'. subread-2.0.3-source/src/input-files.c:4214:10: style: Local variable 'tmp_fname' shadows outer variable [shadowVariable] subread-2.0.3-source/src/input-files.c:4156:7: note: Shadowed declaration subread-2.0.3-source/src/input-files.c:4214:10: note: Shadow variable subread-2.0.3-source/src/input-files.c:5326:7: style: Local variable 'x1' shadows outer variable [shadowVariable] subread-2.0.3-source/src/input-files.c:5303:6: note: Shadowed declaration subread-2.0.3-source/src/input-files.c:5326:7: note: Shadow variable subread-2.0.3-source/src/input-files.c:1234:40: style: Parameter 'key' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:174:35: style: Parameter 'files' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:1399:27: style: Parameter 'sam_line' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:6274:28: style: Parameter 'SAM_line' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:2271:32: style: Parameter 'str' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:3444:70: style: Parameter 'tag_name' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:351:20: style: Parameter 'in_buff' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:3973:41: style: Parameter 'st' can be declared with const [constParameter] subread-2.0.3-source/src/input-files.c:276:21: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:289:22: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:315:12: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:333:12: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:666:5: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:673:3: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:674:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:757:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:952:7: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:955:28: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] subread-2.0.3-source/src/input-files.c:1689:38: portability: 'event_table_ptr->appendix2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/input-files.c:4635:20: portability: 'tab->appendix2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/input-files.c:4656:25: portability: 'tab->appendix2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/input-files.c:1198:23: error: Signed integer overflow for expression '((kv)<'G'?((kv)=='A'?0:2):((kv)=='G'?1:3))<0' is redundant or there is signed integer overflow for expression 'header_txt_dynamic_length-1000000'. [integerOverflowCond] subread-2.0.3-source/src/input-files.c:2950:35: note: Assuming that condition 'header_txt_dynamic_length>0' is not redundant subread-2.0.3-source/src/input-files.c:2950:81: note: Integer overflow subread-2.0.3-source/src/input-files.c:2924:5: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] subread-2.0.3-source/src/input-files.c:2924:5: note: Assignment 'nch=-1', assigned value is -1 subread-2.0.3-source/src/input-files.c:2924:5: note: Negative value is converted to an unsigned value subread-2.0.3-source/src/input-files.c:2925:5: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] subread-2.0.3-source/src/input-files.c:2925:5: note: Assignment 'nch=-1', assigned value is -1 subread-2.0.3-source/src/input-files.c:2925:5: note: Negative value is converted to an unsigned value subread-2.0.3-source/src/input-files.c:2938:5: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] subread-2.0.3-source/src/input-files.c:2938:5: note: Assignment 'nch=-1', assigned value is -1 subread-2.0.3-source/src/input-files.c:2938:5: note: Negative value is converted to an unsigned value subread-2.0.3-source/src/input-files.c:2942:6: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] subread-2.0.3-source/src/input-files.c:2942:6: note: Assignment 'nch=-1', assigned value is -1 subread-2.0.3-source/src/input-files.c:2942:6: note: Negative value is converted to an unsigned value subread-2.0.3-source/src/input-files.c:2961:6: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] subread-2.0.3-source/src/input-files.c:2961:6: note: Assignment 'nch=-1', assigned value is -1 subread-2.0.3-source/src/input-files.c:2961:6: note: Negative value is converted to an unsigned value subread-2.0.3-source/src/input-files.c:107:16: style: Variable 'fpos' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:107:26: style: Variable 'fpos2' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:520:11: style: Variable 'rlen' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:529:11: style: Variable 'rlen' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:882:10: style: Variable 'tr' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:1660:30: style: Variable 'indel_event_id' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:2631:24: style: Variable 'all_orphants' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:2640:16: style: Variable 'all_orphants' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:2919:11: style: Variable 'nch' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:2924:5: style: Variable 'bam_signature' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:4740:6: style: Variable 'x1' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:4906:14: style: Variable 'nch' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:4963:28: style: Variable 'name_len' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:5151:2: style: Variable 'out_bin_ptr' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:5328:3: style: Variable 'bam_signature' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:5561:46: style: Variable 'block_size' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:5585:15: style: Variable 'nch' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:5587:16: style: Variable 'disk_is_full' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/input-files.c:5564:15: style: Variable 'bam_buffer' is allocated memory that is never used. [unusedAllocatedMemory] subread-2.0.3-source/src/readSummary.c:5785:2: error:inconclusive: Address of local auto-variable assigned to a function parameter. [autoVariables] subread-2.0.3-source/src/readSummary.c:1994:4: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/readSummary.c:2000:4: warning: Return value of function deflate() is not used. [ignoredReturnValue] subread-2.0.3-source/src/readSummary.c:3019:4: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/readSummary.c:3024:4: warning: Return value of function deflate() is not used. [ignoredReturnValue] subread-2.0.3-source/src/readSummary.c:5997:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue] subread-2.0.3-source/src/readSummary.c:6005:3: warning: Return value of function deflate() is not used. [ignoredReturnValue] subread-2.0.3-source/src/readSummary.c:4283:15: style: The if condition is the same as the previous if condition [duplicateCondition] subread-2.0.3-source/src/readSummary.c:4281:15: note: First condition subread-2.0.3-source/src/readSummary.c:4283:15: note: Second condition subread-2.0.3-source/src/readSummary.c:7868:29: style: Condition 'c1==c2' is always true [knownConditionTrueFalse] subread-2.0.3-source/src/readSummary.c:7868:15: note: Assuming that condition 'c1=='\t'' is not redundant subread-2.0.3-source/src/readSummary.c:7868:29: note: Condition 'c1==c2' is always true subread-2.0.3-source/src/readSummary.c:7877:20: style: Condition 'c2==0' is always false [knownConditionTrueFalse] subread-2.0.3-source/src/readSummary.c:7877:9: note: Assuming that condition 'c1==0' is not redundant subread-2.0.3-source/src/readSummary.c:7866:9: note: Assuming that condition 'c1!=c2' is not redundant subread-2.0.3-source/src/readSummary.c:7877:20: note: Condition 'c2==0' is always false subread-2.0.3-source/src/readSummary.c:7486:3: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/readSummary.c:8875:4: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] subread-2.0.3-source/src/readSummary.c:987:16: error: Memory leak: file_line [memleak] subread-2.0.3-source/src/readSummary.c:1091:5: error: Common realloc mistake: 'ret_features' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1209:6: error: Common realloc mistake: 'ret_features' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1274:9: error: Common realloc mistake: 'extcols' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1639:6: error: Common realloc mistake: 'ret_block_min_start' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1640:6: error: Common realloc mistake: 'ret_block_max_end' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1641:6: error: Common realloc mistake: 'ret_block_end_index' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1666:5: error: Common realloc mistake: 'ret_block_min_start' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1667:5: error: Common realloc mistake: 'ret_block_max_end' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1668:5: error: Common realloc mistake: 'ret_block_end_index' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:4681:5: error: Common realloc mistake: 'bin_ptrs' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:9150:4: error: Common realloc mistake: 'cmd_rebuilt' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:9488:4: error: Common realloc mistake: 'very_long_file_names' nulled but not freed upon failure [memleakOnRealloc] subread-2.0.3-source/src/readSummary.c:1118:25: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:1115:17: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/readSummary.c:1118:25: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:1119:25: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:1115:36: note: Assuming that condition 'end_ptr==NULL' is not redundant subread-2.0.3-source/src/readSummary.c:1119:25: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:1121:16: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:1115:17: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/readSummary.c:1121:16: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:1218:26: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:1215:18: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/readSummary.c:1218:26: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:1219:26: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:1215:37: note: Assuming that condition 'end_ptr==NULL' is not redundant subread-2.0.3-source/src/readSummary.c:1219:26: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:1221:17: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:1215:18: note: Assuming that condition 'start_ptr==NULL' is not redundant subread-2.0.3-source/src/readSummary.c:1221:17: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:4073:83: warning: Either the condition 'UMI_seq' is redundant or there is possible null pointer dereference: UMI_seq. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:4073:8: note: Assuming that condition 'UMI_seq' is not redundant subread-2.0.3-source/src/readSummary.c:4073:83: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:4073:93: warning: Either the condition 'BC_seq' is redundant or there is possible null pointer dereference: BC_seq. [nullPointerRedundantCheck] subread-2.0.3-source/src/readSummary.c:4073:19: note: Assuming that condition 'BC_seq' is not redundant subread-2.0.3-source/src/readSummary.c:4073:93: note: Null pointer dereference subread-2.0.3-source/src/readSummary.c:4021:24: error: Pointer addition with NULL pointer. [nullPointerArithmetic] subread-2.0.3-source/src/readSummary.c:4146:43: note: Calling function 'scRNA_scan_read_name_str', 2nd argument 'NULL' value is 0 subread-2.0.3-source/src/readSummary.c:4020:23: note: Assuming condition is Assuming condition is false subread-2.0.3-source/src/readSummary.c:4021:24: note: Null pointer addition subread-2.0.3-source/src/readSummary.c:8115:18: style: Variable 'gene_name_tail' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/readSummary.c:8044:18: note: gene_name_tail is assigned subread-2.0.3-source/src/readSummary.c:8115:18: note: gene_name_tail is overwritten subread-2.0.3-source/src/readSummary.c:9568:12: style: Variable 'Rargv[54]' is reassigned a value before the old one has been used. [redundantAssignment] subread-2.0.3-source/src/readSummary.c:9567:12: note: Rargv[54] is assigned subread-2.0.3-source/src/readSummary.c:9568:12: note: Rargv[54] is overwritten subread-2.0.3-source/src/readSummary.c:2311:6: style: Same expression used in consecutive assignments of 'r1_chro' and 'r1_pos'. [duplicateAssignExpression] subread-2.0.3-source/src/readSummary.c:2312:6: note: Same expression used in consecutive assignments of 'r1_chro' and 'r1_pos'. subread-2.0.3-source/src/readSummary.c:2311:6: note: Same expression used in consecutive assignments of 'r1_chro' and 'r1_pos'. subread-2.0.3-source/src/readSummary.c:2312:6: style: Same expression used in consecutive assignments of 'r1_pos' and 'r2_chro'. [duplicateAssignExpression] subread-2.0.3-source/src/readSummary.c:2313:6: note: Same expression used in consecutive assignments of 'r1_pos' and 'r2_chro'. subread-2.0.3-source/src/readSummary.c:2312:6: note: Same expression used in consecutive assignments of 'r1_pos' and 'r2_chro'. subread-2.0.3-source/src/readSummary.c:2313:6: style: Same expression used in consecutive assignments of 'r2_chro' and 'r2_pos'. [duplicateAssignExpression] subread-2.0.3-source/src/readSummary.c:2314:6: note: Same expression used in consecutive assignments of 'r2_chro' and 'r2_pos'. subread-2.0.3-source/src/readSummary.c:2313:6: note: Same expression used in consecutive assignments of 'r2_chro' and 'r2_pos'. subread-2.0.3-source/src/readSummary.c:2314:6: style: Same expression used in consecutive assignments of 'r2_pos' and 'HItag'. [duplicateAssignExpression] subread-2.0.3-source/src/readSummary.c:2315:6: note: Same expression used in consecutive assignments of 'r2_pos' and 'HItag'. subread-2.0.3-source/src/readSummary.c:2314:6: note: Same expression used in consecutive assignments of 'r2_pos' and 'HItag'. subread-2.0.3-source/src/readSummary.c:2657:16: style:inconclusive: Same expression used in consecutive assignments of 'chro_cursor' and 'section_start_chro'. [duplicateAssignExpression] subread-2.0.3-source/src/readSummary.c:2657:38: note: Same expression used in consecutive assignments of 'chro_cursor' and 'section_start_chro'. subread-2.0.3-source/src/readSummary.c:2657:16: note: Same expression used in consecutive assignments of 'chro_cursor' and 'section_start_chro'. subread-2.0.3-source/src/readSummary.c:3142:9: style: The comparison 'ret < 1' is always false. [knownConditionTrueFalse] subread-2.0.3-source/src/readSummary.c:3106:12: note: 'ret' is assigned value '1' here. subread-2.0.3-source/src/readSummary.c:3142:9: note: The comparison 'ret < 1' is always false. subread-2.0.3-source/src/readSummary.c:870:2: style:inconclusive: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode] subread-2.0.3-source/src/readSummary.c:4100:147: style:inconclusive: Function 'add_scRNA_read_tota1_no' argument 4 names different: declaration 'bin1' definition 'bambin'. [funcArgNamesDifferent] subread-2.0.3-source/src/readSummary.c:2903:147: note: Function 'add_scRNA_read_tota1_no' argument 4 names different: declaration 'bin1' definition 'bambin'. subread-2.0.3-source/src/readSummary.c:4100:147: note: Function 'add_scRNA_read_tota1_no' argument 4 names different: declaration 'bin1' definition 'bambin'. subread-2.0.3-source/src/readSummary.c:8992:418: style:inconclusive: Function 'readSummary_single_file' argument 16 names different: declaration 'junc_glob_tab' definition 'junction_global_table'. [funcArgNamesDifferent] subread-2.0.3-source/src/readSummary.c:8170:418: note: Function 'readSummary_single_file' argument 16 names different: declaration 'junc_glob_tab' definition 'junction_global_table'. subread-2.0.3-source/src/readSummary.c:8992:418: note: Function 'readSummary_single_file' argument 16 names different: declaration 'junc_glob_tab' definition 'junction_global_table'. subread-2.0.3-source/src/readSummary.c:8992:453: style:inconclusive: Function 'readSummary_single_file' argument 17 names different: declaration 'splicing_glob_tab' definition 'splicing_global_table'. [funcArgNamesDifferent] subread-2.0.3-source/src/readSummary.c:8170:445: note: Function 'readSummary_single_file' argument 17 names different: declaration 'splicing_glob_tab' definition 'splicing_global_table'. subread-2.0.3-source/src/readSummary.c:8992:453: note: Function 'readSummary_single_file' argument 17 names different: declaration 'splicing_glob_tab' definition 'splicing_global_table'. subread-2.0.3-source/src/readSummary.c:497:7: style: Local variable 'nch' shadows outer variable [shadowVariable] subread-2.0.3-source/src/readSummary.c:434:24: note: Shadowed declaration subread-2.0.3-source/src/readSummary.c:497:7: note: Shadow variable subread-2.0.3-source/src/readSummary.c:2254:8: style: Local variable 'thread_no' shadows outer argument [shadowArgument] subread-2.0.3-source/src/readSummary.c:2178:50: note: Shadowed declaration subread-2.0.3-source/src/readSummary.c:2254:8: note: Shadow variable subread-2.0.3-source/src/readSummary.c:3916:13: style: Local variable 'xx2' shadows outer variable [shadowVariable] subread-2.0.3-source/src/readSummary.c:3890:7: note: Shadowed declaration subread-2.0.3-source/src/readSummary.c:3916:13: note: Shadow variable subread-2.0.3-source/src/readSummary.c:6185:9: style: Local variable 'binlen' shadows outer variable [shadowVariable] subread-2.0.3-source/src/readSummary.c:6153:23: note: Shadowed declaration subread-2.0.3-source/src/readSummary.c:6185:9: note: Shadow variable subread-2.0.3-source/src/readSummary.c:6186:14: style: Local variable 'genes' shadows outer variable [shadowVariable] subread-2.0.3-source/src/readSummary.c:6154:13: note: Shadowed declaration subread-2.0.3-source/src/readSummary.c:6186:14: note: Shadow variable subread-2.0.3-source/src/readSummary.c:6386:23: style: Local variable 'cursor' shadows outer variable [shadowVariable] subread-2.0.3-source/src/readSummary.c:6329:19: note: Shadowed declaration subread-2.0.3-source/src/readSummary.c:6386:23: note: Shadow variable subread-2.0.3-source/src/readSummary.c:6402:23: style: Local variable 'cursor' shadows outer variable [shadowVariable] subread-2.0.3-source/src/readSummary.c:6329:19: note: Shadowed declaration subread-2.0.3-source/src/readSummary.c:6402:23: note: Shadow variable subread-2.0.3-source/src/readSummary.c:371:45: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:427:128: style: Parameter 'cigar' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:427:143: style: Parameter 'extra_tags' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:1730:33: style: Parameter 'rl' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:1868:33: style: Parameter 'n' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:2814:137: style: Parameter 'Starting_Chro_Points_1BASE' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:2814:221: style: Parameter 'Section_Lengths' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:2814:264: style: Parameter 'Event_After_Section' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:2947:74: style: Parameter 'types' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:3759:37: style: Parameter 'x1_bitmap' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:4382:38: style: Parameter 'u1' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:4382:49: style: Parameter 'u2' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:4582:60: style: Parameter 'val' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:4813:155: style: Parameter 'start_poses' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:4813:185: style: Parameter 'lens' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5293:40: style: Parameter 'ky' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5293:50: style: Parameter 'val' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5321:37: style: Parameter 'ky' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5337:51: style: Parameter 'val' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5619:52: style: Parameter 'ky' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5718:45: style: Parameter 'kyGeneID' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5718:62: style: Parameter 'valUMIs' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5760:50: style: Parameter 'k' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5790:71: style: Parameter 'val' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5794:58: style: Parameter 'ky' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5873:46: style: Parameter 'ky_genep1' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5889:47: style: Parameter 'L_elem' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:5889:62: style: Parameter 'R_elem' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:7152:85: style: Parameter 'et_geneid' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:7152:104: style: Parameter 'et_chr' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:7152:123: style: Parameter 'et_start' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:7152:144: style: Parameter 'et_stop' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:7152:169: style: Parameter 'et_strand' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:7152:188: style: Parameter 'et_extra_columns' can be declared with const [constParameter] subread-2.0.3-source/src/readSummary.c:1991:7: portability: 'bin' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:4407:6: portability: 'HashTableGet(cellBCp0_genep0_P1_to_UMIs,NULL+1+(((1LLU*str1->cellbc)<<32)|(str1->gene_no)))' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:4543:45: portability: 'HashTableGet(cellBCp0_genep0_P1_to_UMIs,NULL+1+(((1LLU*str0->cellbc)<<32)|(str0->gene_no)))' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:4605:13: portability: 'vcell_gene' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:5461:67: portability: 'this_bc_pnt_p1' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:5474:86: portability: 'ArrayListGet(sorted_bcno_p1,x1)' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:5553:72: portability: 'ArrayListGet(sorted_idx,x1)' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:5604:49: portability: 'last_ptr' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:5705:52: portability: 'vUMIs' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:6393:17: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:6411:17: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:6470:14: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:6490:14: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer] subread-2.0.3-source/src/readSummary.c:2858:80: error: Uninitialized variable: supported_junctions1 [uninitvar] subread-2.0.3-source/src/readSummary.c:2858:59: error: Uninitialized variable: supported_junctions2 [uninitvar] subread-2.0.3-source/src/readSummary.c:671:18: style: Variable 'nNonExistFiles' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/readSummary.c:1570:35: style: Variable 'sort_i' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/readSummary.c:4304:19: style: Variable 'itemno' is assigned a value that is never used. [unreadVariable] subread-2.0.3-source/src/readSummary.c:8996:30: style: Variable 'line' is allocated memory that is never used. [unusedAllocatedMemory] DONE