2026-01-09 14:25 ftp://ftp.de.debian.org/debian/pool/main/h/htslib/htslib_1.22.1+ds2.orig.tar.bz2 cppcheck-options: --library=posix --library=gnu --library=bsd --library=libcurl --library=zlib --library=openssl --library=bsd --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1 platform: Linux-6.8.0-90-generic-x86_64-with-glibc2.39 python: 3.12.3 client-version: 1.3.69 compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0 cppcheck: head 2.19.0 head-info: 7e723ef (2026-01-09 14:48:21 +0100) count: 766 1662 elapsed-time: 33.4 133.3 head-timing-info: old-timing-info: head results: htslib-1.22.1/htslib/kstring.h:164:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:179:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:241:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:251:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:258:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:267:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:275:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:317:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:373:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:385:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:468:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/kstring.h:492:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/annot-tsv.c:123:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/annot-tsv.c:315:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/annot-tsv.c:997:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/hts.h:1560:12: style: Return value '!(*((char*)(&one)))' is always false [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/htslib/hts.h:1560:12: note: Return value '!(*((char*)(&one)))' is always false htslib-1.22.1/annot-tsv.c:317:19: style: Local variable 'tmp' shadows outer variable [shadowVariable] htslib-1.22.1/annot-tsv.c:296:11: note: Shadowed declaration htslib-1.22.1/annot-tsv.c:317:19: note: Shadow variable htslib-1.22.1/annot-tsv.c:440:40: style: Parameter 'dat' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/annot-tsv.c:495:42: style: Parameter 'str' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/annot-tsv.c:703:53: style: Parameter 'str' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/annot-tsv.c:796:23: style: Variable 'dst' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/annot-tsv.c:797:23: style: Variable 'src' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/annot-tsv.c:856:17: style: Variable 'ann' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/annot-tsv.c:959:26: style: Variable 'loptions' can be declared as const array [constVariable] htslib-1.22.1/htslib/khash_str2int.h:68:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/htslib/khash_str2int.h:131:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/htslib/kstring.h:184:39: style: Parameter 's' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/htslib/kstring.h:200:40: style: Parameter 's' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/textutils_internal.h:361:19: style: Variable 'D' can be declared as const array [constVariable] htslib-1.22.1/htslib/vcf.h:1215:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] htslib-1.22.1/htslib/vcf.h:1318:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bcf_sr_sort.c:220:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/bcf_sr_sort.c:241:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/bcf_sr_sort.c:307:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/bcf_sr_sort.c:326:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/bcf_sr_sort.c:333:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/bcf_sr_sort.c:376:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/bcf_sr_sort.c:324:48: style:inconclusive: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent] htslib-1.22.1/bcf_sr_sort.h:108:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. htslib-1.22.1/bcf_sr_sort.c:324:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. htslib-1.22.1/bcf_sr_sort.c:331:48: style:inconclusive: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent] htslib-1.22.1/bcf_sr_sort.h:111:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. htslib-1.22.1/bcf_sr_sort.c:331:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. htslib-1.22.1/bcf_sr_sort.c:593:85: style:inconclusive: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. [funcArgNamesDifferent] htslib-1.22.1/bcf_sr_sort.h:105:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. htslib-1.22.1/bcf_sr_sort.c:593:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. htslib-1.22.1/bcf_sr_sort.c:43:46: style: Parameter 'bs1' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/bcf_sr_sort.c:43:62: style: Parameter 'bs2' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/bcf_sr_sort.c:224:10: style: Variable 'jmat' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/bcf_sr_sort.c:437:24: style: Variable 'var' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/bcf_sr_sort.c:550:19: style: Variable 'vset' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/htslib/hfile.h:285:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bufsiz [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:368:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:409:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:478:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:505:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:527:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:543:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:1108:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:1545:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:1589:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:1842:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:2213:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:2390:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:2421:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:2488:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:2528:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzf.c:2578:27: style: Expression is always true because 'else if' condition is opposite to previous condition at line 2577. [multiCondition] htslib-1.22.1/bgzf.c:2577:22: note: first condition htslib-1.22.1/bgzf.c:2578:27: note: else if condition is opposite to first condition htslib-1.22.1/bgzf.c:330:9: style: Condition '!ed_is_big()' is always true [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/bgzf.c:330:19: note: Calling function 'ed_is_big' returns 0 htslib-1.22.1/bgzf.c:330:9: note: Condition '!ed_is_big()' is always true htslib-1.22.1/bgzf.c:2366:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/bgzf.c:2366:18: note: Calling function 'ed_is_big' returns 0 htslib-1.22.1/bgzf.c:2366:18: note: Condition 'ed_is_big()' is always false htslib-1.22.1/bgzf.c:2462:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/bgzf.c:2462:18: note: Calling function 'ed_is_big' returns 0 htslib-1.22.1/bgzf.c:2462:18: note: Condition 'ed_is_big()' is always false htslib-1.22.1/bgzf.c:1243:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero] htslib-1.22.1/bgzf.c:533:25: style:inconclusive: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] htslib-1.22.1/htslib/bgzf.h:125:36: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. htslib-1.22.1/bgzf.c:533:25: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. htslib-1.22.1/bgzf.c:618:25: style:inconclusive: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. [funcArgNamesDifferent] htslib-1.22.1/htslib/bgzf.h:392:29: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. htslib-1.22.1/bgzf.c:618:25: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. htslib-1.22.1/bgzf.c:2121:40: style:inconclusive: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. [funcArgNamesDifferent] htslib-1.22.1/htslib/bgzf.h:322:44: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. htslib-1.22.1/bgzf.c:2121:40: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. htslib-1.22.1/bgzf.c:2236:46: style:inconclusive: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. [funcArgNamesDifferent] htslib-1.22.1/htslib/bgzf.h:275:50: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. htslib-1.22.1/bgzf.c:2236:46: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. htslib-1.22.1/bgzf.c:1173:17: style: Local variable 'ret' shadows outer variable [shadowVariable] htslib-1.22.1/bgzf.c:1154:13: note: Shadowed declaration htslib-1.22.1/bgzf.c:1173:17: note: Shadow variable htslib-1.22.1/bgzf.c:1247:18: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/bgzf.c:2604:24: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/bgzf.c:2610:39: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/htslib/hfile.h:134:33: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/htslib/hfile.h:155:34: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/bgzip.c:55:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzip.c:63:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzip.c:70:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzip.c:105:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzip.c:156:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tv_sec [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzip.c:176:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzip.c:255:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] htslib-1.22.1/bgzip.c:159:9: style: Obsolescent function 'utimes' called. It is recommended to use 'utimensat' instead. [prohibitedutimesCalled] htslib-1.22.1/bgzip.c:556:17: style: Local variable 'ret' shadows outer variable [shadowVariable] htslib-1.22.1/bgzip.c:226:51: note: Shadowed declaration htslib-1.22.1/bgzip.c:556:17: note: Shadow variable htslib-1.22.1/bgzip.c:170:11: style: Variable 'ext' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/htslib/sam.h:259:25: error: syntax error [syntaxError] htslib-1.22.1/cram/mFILE.c:157:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] htslib-1.22.1/cram/mFILE.c:182:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/cram/mFILE.c:198:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/cram/mFILE.c:463:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/cram/mFILE.c:520:13: style: Condition 'len!=size*nmemb' is always true [knownConditionTrueFalse] htslib-1.22.1/cram/mFILE.c:511:9: note: len is assigned 'size*nmemb<=mf->size-mf->offset?size*nmemb:mf->size-mf->offset' here. htslib-1.22.1/cram/mFILE.c:514:9: note: Assuming condition is false htslib-1.22.1/cram/mFILE.c:520:13: note: Condition 'len!=size*nmemb' is always true htslib-1.22.1/cram/mFILE.c:264:47: style:inconclusive: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. [funcArgNamesDifferent] htslib-1.22.1/cram/mFILE.h:64:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. htslib-1.22.1/cram/mFILE.c:264:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. htslib-1.22.1/cram/mFILE.c:471:20: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/cram/mFILE.c:494:18: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/cram/mFILE.c:527:22: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/cram/open_trace_file.c:196:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/cram/open_trace_file.c:131:31: style: Condition 'i>0' is always true [knownConditionTrueFalse] htslib-1.22.1/cram/open_trace_file.c:131:20: note: Assuming that condition 'i==0' is not redundant htslib-1.22.1/cram/open_trace_file.c:131:31: note: Condition 'i>0' is always true htslib-1.22.1/cram/open_trace_file.c:204:38: style: Checking if unsigned expression 'mfwrite(buf,len,1,mf)' is less than zero. [unsignedLessThanZero] htslib-1.22.1/cram/open_trace_file.c:182:46: style: Parameter 'url' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/cram/open_trace_file.c:314:53: style: Parameter 'dirname' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/cram/open_trace_file.c:352:48: style: Parameter 'path' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/cram/open_trace_file.c:352:60: style: Parameter 'relative_to' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/cram/open_trace_file.c:445:15: style: Variable 'ele2' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/cram/string_alloc.c:121:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero] htslib-1.22.1/errmod.c:93:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar] htslib-1.22.1/errmod.c:34:1: style: Parameter 'array' can be declared as const array [constParameter] htslib-1.22.1/faidx.c:436:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/faidx.c:473:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/faidx.c:610:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/faidx.c:722:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] htslib-1.22.1/faidx.c:241:31: style: Condition 'c!='\n'' is always true [knownConditionTrueFalse] htslib-1.22.1/faidx.c:239:27: note: Assuming that condition 'c=='+'' is not redundant htslib-1.22.1/faidx.c:241:31: note: Condition 'c!='\n'' is always true htslib-1.22.1/htslib/khash.h:449:10: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory] htslib-1.22.1/faidx.c:100:28: note: Assuming allocation function fails htslib-1.22.1/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0 htslib-1.22.1/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0 htslib-1.22.1/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0 htslib-1.22.1/htslib/khash.h:449:10: note: Null pointer dereference htslib-1.22.1/htslib/khash.h:449:38: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory] htslib-1.22.1/faidx.c:100:28: note: Assuming allocation function fails htslib-1.22.1/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0 htslib-1.22.1/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0 htslib-1.22.1/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0 htslib-1.22.1/htslib/khash.h:449:38: note: Null pointer dereference htslib-1.22.1/faidx.c:142:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory] htslib-1.22.1/faidx.c:141:27: note: Assuming allocation function fails htslib-1.22.1/faidx.c:141:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0 htslib-1.22.1/faidx.c:142:5: note: Null pointer dereference htslib-1.22.1/faidx.c:143:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory] htslib-1.22.1/faidx.c:141:27: note: Assuming allocation function fails htslib-1.22.1/faidx.c:141:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0 htslib-1.22.1/faidx.c:143:5: note: Null pointer dereference htslib-1.22.1/htslib/khash.h:449:13: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] htslib-1.22.1/faidx.c:100:28: note: Assuming allocation function fails htslib-1.22.1/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0 htslib-1.22.1/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0 htslib-1.22.1/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0 htslib-1.22.1/htslib/khash.h:449:13: note: Null pointer addition htslib-1.22.1/faidx.c:728:24: style: Checking if unsigned expression 'val->line_blen' is less than zero. [unsignedLessThanZero] htslib-1.22.1/faidx.c:834:59: style:inconclusive: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] htslib-1.22.1/htslib/faidx.h:201:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:834:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:846:51: style:inconclusive: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] htslib-1.22.1/htslib/faidx.h:192:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:846:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:859:49: style:inconclusive: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] htslib-1.22.1/htslib/faidx.h:190:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:859:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:867:55: style:inconclusive: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] htslib-1.22.1/htslib/faidx.h:217:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:867:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:879:53: style:inconclusive: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] htslib-1.22.1/htslib/faidx.h:215:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:879:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. htslib-1.22.1/faidx.c:919:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/hfile.c:165:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:195:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:238:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:248:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:294:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:328:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:368:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:379:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:390:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:414:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:430:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:451:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:496:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:509:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:551:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:562:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:607:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:626:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:667:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:738:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:766:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:799:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:837:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:883:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:903:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:939:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:1057:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:1159:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile.c:607:17: style: Condition 'ret<0' is always false [knownConditionTrueFalse] htslib-1.22.1/hfile.c:596:15: note: Assignment 'ret=0', assigned value is 0 htslib-1.22.1/hfile.c:607:17: note: Condition 'ret<0' is always false htslib-1.22.1/hfile.c:608:18: style: Condition 'ret<0' is always false [knownConditionTrueFalse] htslib-1.22.1/hfile.c:596:15: note: Assignment 'ret=0', assigned value is 0 htslib-1.22.1/hfile.c:608:18: note: Condition 'ret<0' is always false htslib-1.22.1/hfile.c:1050:57: style: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true [knownConditionTrueFalse] htslib-1.22.1/hfile.c:1050:39: note: Calling function 'try_exe_add_scheme_handler' returns -1 htslib-1.22.1/hfile.c:1050:57: note: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true htslib-1.22.1/hfile.c:1305:26: style:inconclusive: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hfile.h:74:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. htslib-1.22.1/hfile.c:1305:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. htslib-1.22.1/hfile.c:1333:27: style:inconclusive: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hfile.h:99:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. htslib-1.22.1/hfile.c:1333:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. htslib-1.22.1/hfile.c:1353:46: style:inconclusive: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hfile.h:114:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. htslib-1.22.1/hfile.c:1353:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. htslib-1.22.1/hfile.c:171:50: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/hfile.c:243:11: style: Variable 'found' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/hfile.c:580:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/hfile.c:594:28: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'fd_flush' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/hfile.c:632:33: note: You might need to cast the function pointer here htslib-1.22.1/hfile.c:594:28: note: Parameter 'fpv' can be declared as pointer to const htslib-1.22.1/hfile.c:614:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/hfile.c:797:30: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'mem_seek' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/hfile.c:810:17: note: You might need to cast the function pointer here htslib-1.22.1/hfile.c:797:30: note: Parameter 'fpv' can be declared as pointer to const htslib-1.22.1/hfile.c:803:29: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'mem_close' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/hfile.c:810:33: note: You might need to cast the function pointer here htslib-1.22.1/hfile.c:803:29: note: Parameter 'fpv' can be declared as pointer to const htslib-1.22.1/hfile.c:881:35: style: Parameter 'file' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/hfile.c:1291:31: style: Variable 'p' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/hfile.c:1391:9: style: struct member 'knetFile_s::type' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1393:11: style: struct member 'knetFile_s::host' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1393:18: style: struct member 'knetFile_s::port' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1394:9: style: struct member 'knetFile_s::ctrl_fd' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1394:18: style: struct member 'knetFile_s::pasv_ip' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1394:30: style: struct member 'knetFile_s::pasv_port' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1394:41: style: struct member 'knetFile_s::max_response' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1394:55: style: struct member 'knetFile_s::no_reconnect' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1394:69: style: struct member 'knetFile_s::is_ready' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1395:11: style: struct member 'knetFile_s::response' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1395:22: style: struct member 'knetFile_s::retr' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1395:29: style: struct member 'knetFile_s::size_cmd' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1396:13: style: struct member 'knetFile_s::seek_offset' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1397:13: style: struct member 'knetFile_s::file_size' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1398:11: style: struct member 'knetFile_s::path' is never used. [unusedStructMember] htslib-1.22.1/hfile.c:1398:18: style: struct member 'knetFile_s::http_host' is never used. [unusedStructMember] htslib-1.22.1/hfile_gcs.c:75:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_gcs.c:104:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] htslib-1.22.1/hfile_gcs.c:105:24: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] htslib-1.22.1/hfile_gcs.c:112:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] htslib-1.22.1/hfile_libcurl.c:131:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOSYS [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:160:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:240:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EBADF [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:282:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:315:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:329:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:370:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:513:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:568:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:701:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLM_OK [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:750:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_WRITEFUNC_PAUSE [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:767:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:826:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:870:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_READFUNC_PAUSE [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:889:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:934:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:1016:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:1134:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:1188:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:1437:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:1522:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_GLOBAL_ALL [valueFlowBailoutIncompleteVar] htslib-1.22.1/hfile_libcurl.c:797:23: style: Condition 'bytesfd_sent==end' is always false [knownConditionTrueFalse] htslib-1.22.1/ref_cache/transaction.c:602:35: note: Assuming that condition 'transact->fd_sentfd_sent==end' is always false htslib-1.22.1/ref_cache/transaction.c:775:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] htslib-1.22.1/ref_cache/transaction.c:433:27: warning: If memory allocation fails, then there is a possible null pointer dereference: text [nullPointerOutOfMemory] htslib-1.22.1/ref_cache/transaction.c:428:18: note: Assuming allocation function fails htslib-1.22.1/ref_cache/transaction.c:428:18: note: Assignment 'text=malloc(text_len)', assigned value is 0 htslib-1.22.1/ref_cache/transaction.c:433:27: note: Null pointer dereference htslib-1.22.1/ref_cache/transaction.c:446:17: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] htslib-1.22.1/ref_cache/transaction.c:428:18: note: Assuming allocation function fails htslib-1.22.1/ref_cache/transaction.c:428:18: note: Assignment 'text=malloc(text_len)', assigned value is 0 htslib-1.22.1/ref_cache/transaction.c:446:17: note: Null pointer addition htslib-1.22.1/ref_cache/transaction.c:210:46: style: Parameter 'transact' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/transaction.c:214:45: style: Parameter 'transact' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/transaction.c:225:52: style: Parameter 'transact' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/transaction.c:313:58: style: Parameter 'transact' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/transaction.c:619:43: style: Parameter 'transact' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/transaction.c:469:16: style: Variable 'iovcnt' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/ref_cache/upstream.c:132:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable iov_base [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:155:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable iov_base [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:184:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable iov_base [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:225:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable iov_base [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:257:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:401:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_URL [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:480:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:638:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:694:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLINFO_RESPONSE_CODE [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:761:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_POLL_REMOVE [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:813:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:865:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:905:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:926:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:1002:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLM_CALL_MULTI_PERFORM [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:1075:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:1163:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIG_IGN [valueFlowBailoutIncompleteVar] htslib-1.22.1/ref_cache/upstream.c:785:31: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck] htslib-1.22.1/ref_cache/upstream.c:797:23: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck] htslib-1.22.1/ref_cache/upstream.c:874:12: style: Variable 'cc' is reassigned a value before the old one has been used. [redundantAssignment] htslib-1.22.1/ref_cache/upstream.c:869:12: note: cc is assigned htslib-1.22.1/ref_cache/upstream.c:874:12: note: cc is overwritten htslib-1.22.1/ref_cache/upstream.c:215:49: style:inconclusive: Function 'upstream_recv_msg' argument 2 names different: declaration 'msg' definition 'umsg'. [funcArgNamesDifferent] htslib-1.22.1/ref_cache/upstream.h:46:49: note: Function 'upstream_recv_msg' argument 2 names different: declaration 'msg' definition 'umsg'. htslib-1.22.1/ref_cache/upstream.c:215:49: note: Function 'upstream_recv_msg' argument 2 names different: declaration 'msg' definition 'umsg'. htslib-1.22.1/ref_cache/upstream.c:785:58: style: Clarify calculation precedence for '|' and '?'. [clarifyCalculation] htslib-1.22.1/ref_cache/upstream.c:797:50: style: Clarify calculation precedence for '|' and '?'. [clarifyCalculation] htslib-1.22.1/ref_cache/upstream.c:206:17: style: Variable 'd' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/ref_cache/upstream.c:252:33: style: Parameter 'opts' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/upstream.c:252:45: style: Parameter 'hexmd5' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/upstream.c:306:33: style: Parameter 'opts' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/upstream.c:306:63: style: Parameter 'hexmd5' can be declared as const array [constParameter] htslib-1.22.1/ref_cache/upstream.c:635:41: style: Parameter 'downstream' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/upstream.c:669:15: style: Variable 'download' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/ref_cache/upstream.c:1047:67: style: Parameter 'cmd_fds' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/ref_cache/upstream.c:1088:22: style: Variable 'polled' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/ref_cache/upstream.c:1161:29: style: Variable 'cvi' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/regidx.c:164:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/regidx.c:440:68: style: Condition 'list->reg[ireg].beg<=end' is always true [knownConditionTrueFalse] htslib-1.22.1/regidx.c:439:38: note: Assuming that condition 'list->reg[ireg].beg>end' is not redundant htslib-1.22.1/regidx.c:440:68: note: Condition 'list->reg[ireg].beg<=end' is always true htslib-1.22.1/regidx.c:631:63: style: Condition 'list->reg[i].beg<=itr->end' is always true [knownConditionTrueFalse] htslib-1.22.1/regidx.c:630:31: note: Assuming that condition 'list->reg[i].beg>itr->end' is not redundant htslib-1.22.1/regidx.c:631:63: note: Condition 'list->reg[i].beg<=itr->end' is always true htslib-1.22.1/regidx.c:209:42: style:inconclusive: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:150:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. htslib-1.22.1/regidx.c:209:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. htslib-1.22.1/regidx.c:209:119: style:inconclusive: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:150:121: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. htslib-1.22.1/regidx.c:209:119: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. htslib-1.22.1/regidx.c:246:114: style:inconclusive: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:148:113: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. htslib-1.22.1/regidx.c:246:114: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. htslib-1.22.1/regidx.c:401:30: style:inconclusive: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:167:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. htslib-1.22.1/regidx.c:401:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. htslib-1.22.1/regidx.c:401:95: style:inconclusive: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:167:92: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:401:95: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:584:33: style:inconclusive: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:212:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. htslib-1.22.1/regidx.c:584:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. htslib-1.22.1/regidx.c:599:29: style:inconclusive: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:216:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. htslib-1.22.1/regidx.c:599:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. htslib-1.22.1/regidx.c:599:47: style:inconclusive: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:216:44: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:599:47: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:606:31: style:inconclusive: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:214:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:606:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:612:30: style:inconclusive: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:223:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:612:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:646:27: style:inconclusive: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/regidx.h:230:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:646:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. htslib-1.22.1/regidx.c:105:35: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/regidx.c:132:35: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/regidx.c:132:45: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/regidx.c:151:38: style: Parameter 'chr_beg' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/regidx.c:151:53: style: Parameter 'chr_end' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/regidx.c:151:98: style: Parameter 'payload' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/regidx.c:684:13: style: Variable 'src_itr' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/regidx.c:48:15: style: struct member 'pos_t::pos' is never used. [unusedStructMember] htslib-1.22.1/regidx.c:49:15: style: struct member 'pos_t::ireg' is never used. [unusedStructMember] htslib-1.22.1/region.c:43:21: style: Variable 'a' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/region.c:44:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/region.c:87:35: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/samples/add_header.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/cram.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/cram.c:53:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/dump_aux.c:126:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/dump_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/flags_demo.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/flags_demo.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/flags_htsopt_field.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/flags_htsopt_field.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/index_fasta.c:57:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/index_fasta.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/index_multireg_read.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/index_multireg_read.c:117:12: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition] htslib-1.22.1/samples/index_multireg_read.c:74:9: warning: If memory allocation fails, then there is a possible null pointer dereference: regions [nullPointerOutOfMemory] htslib-1.22.1/samples/index_multireg_read.c:70:21: note: Assuming allocation function fails htslib-1.22.1/samples/index_multireg_read.c:70:21: note: Assignment 'regions=calloc(regcnt,sizeof(char*))', assigned value is 0 htslib-1.22.1/samples/index_multireg_read.c:74:9: note: Null pointer dereference htslib-1.22.1/samples/index_reg_read.c:68:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/index_write.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/mod_aux.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/mod_aux.c:116:27: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast] htslib-1.22.1/samples/mod_aux_ba.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/mod_aux_ba.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/mod_bam.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/modstate.c:64:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/modstate.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/modstate.c:56:77: style: Variable 'bm' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/samples/mpileup.c:96:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/mpileup.c:56:26: style: Parameter 'data' can be declared as pointer to const. However it seems that 'plpconstructor' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/mpileup.c:138:36: note: You might need to cast the function pointer here htslib-1.22.1/samples/mpileup.c:56:26: note: Parameter 'data' can be declared as pointer to const htslib-1.22.1/samples/mpileup.c:56:64: style: Parameter 'cd' can be declared as pointer to const. However it seems that 'plpconstructor' is a callback function, if 'cd' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/mpileup.c:138:36: note: You might need to cast the function pointer here htslib-1.22.1/samples/mpileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const htslib-1.22.1/samples/mpileup.c:60:25: style: Parameter 'data' can be declared as pointer to const. However it seems that 'plpdestructor' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/mpileup.c:139:35: note: You might need to cast the function pointer here htslib-1.22.1/samples/mpileup.c:60:25: note: Parameter 'data' can be declared as pointer to const htslib-1.22.1/samples/mpileup.c:60:63: style: Parameter 'cd' can be declared as pointer to const. However it seems that 'plpdestructor' is a callback function, if 'cd' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/mpileup.c:139:35: note: You might need to cast the function pointer here htslib-1.22.1/samples/mpileup.c:60:63: note: Parameter 'cd' can be declared as pointer to const htslib-1.22.1/samples/pileup.c:104:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/pileup.c:56:26: style: Parameter 'data' can be declared as pointer to const. However it seems that 'plpconstructor' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/pileup.c:131:34: note: You might need to cast the function pointer here htslib-1.22.1/samples/pileup.c:56:26: note: Parameter 'data' can be declared as pointer to const htslib-1.22.1/samples/pileup.c:56:64: style: Parameter 'cd' can be declared as pointer to const. However it seems that 'plpconstructor' is a callback function, if 'cd' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/pileup.c:131:34: note: You might need to cast the function pointer here htslib-1.22.1/samples/pileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const htslib-1.22.1/samples/pileup.c:65:25: style: Parameter 'data' can be declared as pointer to const. However it seems that 'plpdestructor' is a callback function, if 'data' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/pileup.c:132:33: note: You might need to cast the function pointer here htslib-1.22.1/samples/pileup.c:65:25: note: Parameter 'data' can be declared as pointer to const htslib-1.22.1/samples/pileup.c:65:63: style: Parameter 'cd' can be declared as pointer to const. However it seems that 'plpdestructor' is a callback function, if 'cd' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/samples/pileup.c:132:33: note: You might need to cast the function pointer here htslib-1.22.1/samples/pileup.c:65:63: note: Parameter 'cd' can be declared as pointer to const htslib-1.22.1/samples/pileup_mod.c:109:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/qtask_ordered.c:157:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qseq [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/qtask_ordered.c:198:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/qtask_ordered.c:241:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/qtask_ordered.c:164:78: portability:inconclusive: Casting from float * to const unsigned char * is not portable due to different binary data representations on different platforms. [invalidPointerCast] htslib-1.22.1/samples/qtask_ordered.c:148:14: style: Variable 'data' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/samples/qtask_ordered.c:223:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/qtask_ordered.c:145:20: style: Variable 'pos' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/samples/qtask_ordered.c:147:19: style: Variable 'gcratio' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/samples/qtask_ordered.c:156:14: style: Variable 'data' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/samples/qtask_ordered.c:181:11: style: Variable 'i' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/samples/qtask_unordered.c:157:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qseq [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/qtask_unordered.c:196:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/qtask_unordered.c:153:14: style: Variable 'data' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/samples/qtask_unordered.c:181:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/qtask_unordered.c:152:18: style: Variable 'pos' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/samples/qtask_unordered.c:156:14: style: Variable 'data' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/samples/read_aux.c:122:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/read_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/read_bam.c:63:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/read_bam.c:114:18: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/samples/read_bam.c:55:20: note: Shadowed declaration htslib-1.22.1/samples/read_bam.c:114:18: note: Shadow variable htslib-1.22.1/samples/read_bam.c:48:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/read_fast.c:58:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/read_fast.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/read_fast_index.c:58:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FAI_FASTA [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/read_fast_index.c:53:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/read_header.c:56:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/read_refname.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/read_refname.c:91:13: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition] htslib-1.22.1/samples/read_refname.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/rem_header.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/rem_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/split.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/split.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/split2.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/split2.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/split_thread1.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/split_thread1.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/split_thread2.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/split_thread2.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/update_header.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/update_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/samples/write_fast.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] htslib-1.22.1/samples/write_fast.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter] htslib-1.22.1/synced_bcf_reader.c:89:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:129:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pair [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:204:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:223:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable targets_overlap [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:455:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:482:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable closefile [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:503:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable closefile [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:719:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:812:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:910:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:1051:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:1493:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/synced_bcf_reader.c:454:5: warning: If memory allocation fails, then there is a possible null pointer dereference: files [nullPointerOutOfMemory] htslib-1.22.1/synced_bcf_reader.c:453:43: note: Assuming allocation function fails htslib-1.22.1/synced_bcf_reader.c:453:24: note: Assignment 'files=(struct bcf_srs_t*)calloc(1,sizeof(struct bcf_srs_t))', assigned value is 0 htslib-1.22.1/synced_bcf_reader.c:454:5: note: Null pointer dereference htslib-1.22.1/synced_bcf_reader.c:455:23: warning: If memory allocation fails, then there is a possible null pointer dereference: files [nullPointerOutOfMemory] htslib-1.22.1/synced_bcf_reader.c:453:43: note: Assuming allocation function fails htslib-1.22.1/synced_bcf_reader.c:453:24: note: Assignment 'files=(struct bcf_srs_t*)calloc(1,sizeof(struct bcf_srs_t))', assigned value is 0 htslib-1.22.1/synced_bcf_reader.c:455:23: note: Null pointer dereference htslib-1.22.1/synced_bcf_reader.c:252:34: style:inconclusive: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:239:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:252:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:274:35: style:inconclusive: Function 'bcf_sr_add_hreader' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:257:35: note: Function 'bcf_sr_add_hreader' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:274:35: note: Function 'bcf_sr_add_hreader' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:479:32: style:inconclusive: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:205:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:479:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:865:33: style:inconclusive: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:272:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:865:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:936:35: style:inconclusive: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:302:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:936:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. htslib-1.22.1/synced_bcf_reader.c:936:54: style:inconclusive: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:302:56: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. htslib-1.22.1/synced_bcf_reader.c:936:54: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. htslib-1.22.1/synced_bcf_reader.c:1243:77: style:inconclusive: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:369:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. htslib-1.22.1/synced_bcf_reader.c:1243:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. htslib-1.22.1/synced_bcf_reader.c:1243:87: style:inconclusive: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:369:86: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. htslib-1.22.1/synced_bcf_reader.c:1243:87: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. htslib-1.22.1/synced_bcf_reader.c:1243:98: style:inconclusive: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:369:96: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. htslib-1.22.1/synced_bcf_reader.c:1243:98: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. htslib-1.22.1/synced_bcf_reader.c:1322:47: style:inconclusive: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:372:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. htslib-1.22.1/synced_bcf_reader.c:1322:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. htslib-1.22.1/synced_bcf_reader.c:1347:43: style:inconclusive: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:381:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. htslib-1.22.1/synced_bcf_reader.c:1347:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. htslib-1.22.1/synced_bcf_reader.c:1347:60: style:inconclusive: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:381:64: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. htslib-1.22.1/synced_bcf_reader.c:1347:60: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. htslib-1.22.1/synced_bcf_reader.c:1554:44: style:inconclusive: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. [funcArgNamesDifferent] htslib-1.22.1/htslib/synced_bcf_reader.h:411:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. htslib-1.22.1/synced_bcf_reader.c:1554:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. htslib-1.22.1/synced_bcf_reader.c:1516:33: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] htslib-1.22.1/synced_bcf_reader.c:150:37: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/synced_bcf_reader.c:416:20: style: Variable 'hdr0' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/synced_bcf_reader.c:417:20: style: Variable 'hdr1' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/synced_bcf_reader.c:542:40: style: Parameter 'reader' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/synced_bcf_reader.c:542:56: style: Parameter 'line' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/synced_bcf_reader.c:635:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/synced_bcf_reader.c:636:19: style: Variable 'alt' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/synced_bcf_reader.c:1061:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/synced_bcf_reader.c:1062:16: style: Variable 'b' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/synced_bcf_reader.c:1392:20: style: Variable 'creg' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/tbx.c:577:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/tbx.c:387:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/tbx.c:387:18: note: Calling function 'ed_is_big' returns 0 htslib-1.22.1/tbx.c:387:18: note: Condition 'ed_is_big()' is always false htslib-1.22.1/tbx.c:113:27: style: Local variable 't' shadows outer variable [shadowVariable] htslib-1.22.1/tbx.c:100:15: note: Shadowed declaration htslib-1.22.1/tbx.c:113:27: note: Shadow variable htslib-1.22.1/tbx.c:160:31: style: Local variable 't' shadows outer variable [shadowVariable] htslib-1.22.1/tbx.c:100:15: note: Shadowed declaration htslib-1.22.1/tbx.c:160:31: note: Shadow variable htslib-1.22.1/tbx.c:392:13: style: Local variable 'x' shadows outer variable [shadowVariable] htslib-1.22.1/tbx.c:370:14: note: Shadowed declaration htslib-1.22.1/tbx.c:392:13: note: Shadow variable htslib-1.22.1/tbx.c:78:19: style: Variable 'ss_dup' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/tbx.c:548:11: style: Variable 'nm' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/tbx.c:102:52: style: Variable 'tmp' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/tbx.c:114:36: style: Variable 'nodeid' is assigned a value that is never used. [unreadVariable] htslib-1.22.1/test/hfile.c:41:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hfile.c:57:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hfile.c:108:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hts_endian.c:169:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hts_endian.c:252:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hts_endian.c:333:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hts_endian.c:415:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hts_endian.c:460:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hts_endian.c:508:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/hts_endian.c:149:31: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/test/test-bcf-sr.c:49:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-bcf-sr.c:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-bcf-sr.c:150:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-bcf-sr.c:78:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/test/test-bcf-sr.c:95:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/test/test-bcf-sr.c:128:26: style: Variable 'loptions' can be declared as const array [constVariable] htslib-1.22.1/test/test-bcf-translate.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-bcf-translate.c:114:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-regidx.c:50:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-regidx.c:60:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-regidx.c:69:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-regidx.c:193:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-regidx.c:417:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-regidx.c:441:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-regidx.c:92:11: style: Variable 'se' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/test/test-regidx.c:250:11: style: Variable 'beg' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/test/test-regidx.c:307:53: style: Parameter 'chr' can be declared as pointer to const. However it seems that 'create_line_bed' is a callback function, if 'chr' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/test/test-regidx.c:457:10: note: You might need to cast the function pointer here htslib-1.22.1/test/test-regidx.c:307:53: note: Parameter 'chr' can be declared as pointer to const htslib-1.22.1/test/test-regidx.c:311:53: style: Parameter 'chr' can be declared as pointer to const. However it seems that 'create_line_tab' is a callback function, if 'chr' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/test/test-regidx.c:451:10: note: You might need to cast the function pointer here htslib-1.22.1/test/test-regidx.c:311:53: note: Parameter 'chr' can be declared as pointer to const htslib-1.22.1/test/test-regidx.c:315:53: style: Parameter 'chr' can be declared as pointer to const. However it seems that 'create_line_reg' is a callback function, if 'chr' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/test/test-regidx.c:454:10: note: You might need to cast the function pointer here htslib-1.22.1/test/test-regidx.c:315:53: note: Parameter 'chr' can be declared as pointer to const htslib-1.22.1/test/test-regidx.c:428:26: style: Variable 'loptions' can be declared as const array [constVariable] htslib-1.22.1/test/test-vcf-api.c:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:52:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:112:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:288:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:407:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:435:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:493:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:547:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:586:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:720:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test-vcf-api.c:52:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] htslib-1.22.1/test/test-vcf-api.c:203:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] htslib-1.22.1/test/test-vcf-api.c:202:34: note: Assuming allocation function fails htslib-1.22.1/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 htslib-1.22.1/test/test-vcf-api.c:203:5: note: Null pointer dereference htslib-1.22.1/test/test-vcf-api.c:204:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] htslib-1.22.1/test/test-vcf-api.c:202:34: note: Assuming allocation function fails htslib-1.22.1/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 htslib-1.22.1/test/test-vcf-api.c:204:5: note: Null pointer dereference htslib-1.22.1/test/test-vcf-api.c:205:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] htslib-1.22.1/test/test-vcf-api.c:202:34: note: Assuming allocation function fails htslib-1.22.1/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 htslib-1.22.1/test/test-vcf-api.c:205:5: note: Null pointer dereference htslib-1.22.1/test/test-vcf-api.c:206:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] htslib-1.22.1/test/test-vcf-api.c:202:34: note: Assuming allocation function fails htslib-1.22.1/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 htslib-1.22.1/test/test-vcf-api.c:206:5: note: Null pointer dereference htslib-1.22.1/test/test-vcf-api.c:207:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] htslib-1.22.1/test/test-vcf-api.c:202:34: note: Assuming allocation function fails htslib-1.22.1/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 htslib-1.22.1/test/test-vcf-api.c:207:5: note: Null pointer dereference htslib-1.22.1/test/test-vcf-api.c:208:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] htslib-1.22.1/test/test-vcf-api.c:202:34: note: Assuming allocation function fails htslib-1.22.1/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 htslib-1.22.1/test/test-vcf-api.c:208:5: note: Null pointer dereference htslib-1.22.1/test/test-vcf-api.c:254:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpfa [nullPointerOutOfMemory] htslib-1.22.1/test/test-vcf-api.c:253:34: note: Assuming allocation function fails htslib-1.22.1/test/test-vcf-api.c:253:20: note: Assignment 'tmpfa=(float*)malloc(2*sizeof(float))', assigned value is 0 htslib-1.22.1/test/test-vcf-api.c:254:5: note: Null pointer dereference htslib-1.22.1/test/test-vcf-api.c:69:44: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/test/test-vcf-api.c:357:17: style: Variable 'tmpia' can be declared as const array [constVariable] htslib-1.22.1/test/test-vcf-sweep.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:71:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:81:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:93:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:113:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:125:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:168:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:184:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:194:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:207:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:218:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:238:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:248:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:270:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:281:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:291:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:302:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:318:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:332:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:367:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:408:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:444:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:524:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:590:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:623:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:646:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:741:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:842:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:886:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:931:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:992:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:1078:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_bgzf.c:518:56: warning: Either the condition 'pos=5' is always false [knownConditionTrueFalse] htslib-1.22.1/test/test_kstring.c:309:26: note: Assignment 'valm=-val', assigned value is less than 1 htslib-1.22.1/test/test_kstring.c:310:44: note: Condition 'valm>=5' is always false htslib-1.22.1/test/test_kstring.c:462:17: style: Variable 'tdata' can be declared as const array [constVariable] htslib-1.22.1/test/test_kstring.c:518:17: style: Variable 'tdata' can be declared as const array [constVariable] htslib-1.22.1/test/test_kstring.c:586:11: style: Variable 'test' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/test/test_kstring.c:458:13: style: struct member 'data::pos' is never used. [unusedStructMember] htslib-1.22.1/test/test_kstring.c:514:13: style: struct member 'data::pos' is never used. [unusedStructMember] htslib-1.22.1/test/test_str2int.c:59:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_str2int.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_str2int.c:160:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_str2int.c:166:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_str2int.c:200:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_str2int.c:217:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/hts_time_funcs.h:168:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_time_funcs.c:44:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_time_funcs.c:58:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/test_time_funcs.c:41:15: portability: Non reentrant function 'gmtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'gmtime_r'. [prohibitedgmtimeCalled] htslib-1.22.1/hts_time_funcs.h:139:9: style: Variable 'month_start' can be declared as const array [constVariable] htslib-1.22.1/test/thrash_threads1.c:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/thrash_threads3.c:38:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/thrash_threads4.c:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/thrash_threads5.c:40:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/thrash_threads6.c:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/thrash_threads7.c:87:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] htslib-1.22.1/test/thrash_threads7.c:44:19: style: Variable 'usecs' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/thread_pool.c:756:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_RECURSIVE [valueFlowBailoutIncompleteVar] htslib-1.22.1/thread_pool.c:860:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] htslib-1.22.1/thread_pool.c:1052:36: style: Condition 'hts_tpool_process_flush(q)!=0' is always false [knownConditionTrueFalse] htslib-1.22.1/thread_pool.c:1052:32: note: Calling function 'hts_tpool_process_flush' returns 0 htslib-1.22.1/thread_pool.c:1052:36: note: Condition 'hts_tpool_process_flush(q)!=0' is always false htslib-1.22.1/thread_pool.c:56:36: style:inconclusive: Function 'hts_tpool_worker_id' argument 1 names different: declaration 'pool' definition 'p'. [funcArgNamesDifferent] htslib-1.22.1/htslib/thread_pool.h:124:36: note: Function 'hts_tpool_worker_id' argument 1 names different: declaration 'pool' definition 'p'. htslib-1.22.1/thread_pool.c:56:36: note: Function 'hts_tpool_worker_id' argument 1 names different: declaration 'pool' definition 'p'. htslib-1.22.1/thread_pool.c:56:36: style: Parameter 'p' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/thread_pool.c:358:47: style: Parameter 'r' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/thread_pool.c:477:43: style: Variable 'first' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/thread_pool.c:819:31: style: Parameter 'p' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/thread_pool.c:1081:48: style: Parameter 'q' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/vcf_sweep.c:82:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/vcf_sweep.c:106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/vcf_sweep.c:174:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] htslib-1.22.1/vcf_sweep.c:117:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:117:5: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:118:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:118:5: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:118:30: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:118:30: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:119:9: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:119:9: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:120:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:120:5: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:120:29: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:120:29: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:121:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:121:5: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:122:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:122:5: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:122:33: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:122:33: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:123:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:123:5: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:124:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] htslib-1.22.1/vcf_sweep.c:116:44: note: Assuming allocation function fails htslib-1.22.1/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 htslib-1.22.1/vcf_sweep.c:124:5: note: Null pointer dereference htslib-1.22.1/vcf_sweep.c:58:45: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/vcf_sweep.c:64:11: style: Variable 't' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcf_sweep.c:189:39: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer] htslib-1.22.1/vcfutils.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] htslib-1.22.1/vcfutils.c:216:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] htslib-1.22.1/vcfutils.c:303:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable info [valueFlowBailoutIncompleteVar] htslib-1.22.1/vcfutils.c:463:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] htslib-1.22.1/vcfutils.c:497:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] htslib-1.22.1/vcfutils.c:775:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] htslib-1.22.1/vcfutils.c:829:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] htslib-1.22.1/vcfutils.c:134:55: style:inconclusive: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcfutils.h:117:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. htslib-1.22.1/vcfutils.c:134:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. htslib-1.22.1/vcfutils.c:134:66: style:inconclusive: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcfutils.h:117:65: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. htslib-1.22.1/vcfutils.c:134:66: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. htslib-1.22.1/vcfutils.c:241:67: style:inconclusive: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcfutils.h:61:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. htslib-1.22.1/vcfutils.c:241:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. htslib-1.22.1/vcfutils.c:43:13: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/vcfutils.c:34:9: note: Shadowed declaration htslib-1.22.1/vcfutils.c:43:13: note: Shadow variable htslib-1.22.1/vcfutils.c:96:13: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/vcfutils.c:34:9: note: Shadowed declaration htslib-1.22.1/vcfutils.c:96:13: note: Shadow variable htslib-1.22.1/vcfutils.c:579:17: style: Local variable 'size' shadows outer variable [shadowVariable] htslib-1.22.1/vcfutils.c:563:13: note: Shadowed declaration htslib-1.22.1/vcfutils.c:579:17: note: Shadow variable htslib-1.22.1/vcfutils.c:44:18: style: Variable 'ac_ptr' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:462:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:463:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:496:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:497:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:624:56: style: Variable 'se' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:774:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:775:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:828:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/vcfutils.c:829:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] htslib-1.22.1/htslib/khash.h:449:10: warning: Null pointer dereference: s [ctunullpointer] htslib-1.22.1/bcf_sr_sort.c:451:59: note: Assuming allocation function fails htslib-1.22.1/bcf_sr_sort.c:451:59: note: Calling function 'khash_str2int_set', 2nd argument 'strdup(var_str)' value is 0 htslib-1.22.1/htslib/khash_str2int.h:119:10: note: Assuming condition is false htslib-1.22.1/htslib/khash_str2int.h:120:9: note: Calling function kh_put_str2int, 2nd argument is null htslib-1.22.1/htslib/khash_str2int.h:30:1: note: Calling function __ac_FNV1a_hash_string, 1st argument is null htslib-1.22.1/htslib/khash.h:449:10: note: Dereferencing argument s that is null htslib-1.22.1/htslib/khash_str2int.h:30:1: warning: Null pointer dereference: empty [ctunullpointer] htslib-1.22.1/bcf_sr_sort.c:451:59: note: Assuming allocation function fails htslib-1.22.1/bcf_sr_sort.c:451:34: note: Calling function khash_str2int_set, 2nd argument is null htslib-1.22.1/htslib/khash_str2int.h:120:9: note: Calling function kh_put_str2int, 2nd argument is null htslib-1.22.1/htslib/khash_str2int.h:30:1: note: Dereferencing argument empty that is null htslib-1.22.1/faidx.c:76:1: warning: If memory allocation fails, then there is a possible null pointer dereference: empty [ctunullpointerOutOfMemory] htslib-1.22.1/faidx.c:100:28: note: Assuming allocation function fails htslib-1.22.1/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0 htslib-1.22.1/faidx.c:102:17: note: Calling function kh_put_s, 2nd argument is null htslib-1.22.1/faidx.c:76:1: note: Dereferencing argument empty that is null diff: 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1003:35: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_const_encode' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1003:35: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1003:54: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_const_encode' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1003:54: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1004:29: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_const_encode' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1004:29: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1008:65: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_const_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4017:20: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1008:65: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1031:48: style: Parameter 'st' can be declared as pointer to const. However it seems that 'cram_const_encode_init' is a callback function, if 'st' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:3896:5: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1031:48: note: Parameter 'st' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1055:93: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_beta_decode_long' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4099:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1055:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1073:92: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_beta_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4097:26: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1073:92: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1091:93: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_beta_decode_char' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4101:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1091:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1167:34: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_beta_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4096:20: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1167:34: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1192:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1204:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1216:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1327:94: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xpack_decode_long' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4112:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1327:94: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1342:93: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xpack_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4114:30: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1342:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1391:94: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xpack_decode_char' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4116:30: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1391:94: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1456:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1521:35: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_xpack_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4111:19: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1521:35: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1566:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1577:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1587:34: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xpack_encode_char' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4117:24: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1587:34: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1641:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1661:60: error: Shifting signed 32-bit value by 31 bits is undefined behaviour [shiftTooManyBitsSigned] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1667:41: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_long' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1667:41: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1667:60: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_long' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1667:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1667:75: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_long' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1667:75: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1667:85: style: Parameter 'out' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_long' is a callback function, if 'out' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1667:85: note: Parameter 'out' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1667:95: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_long' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1667:95: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1671:94: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1780:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1671:94: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1688:55: style: Parameter 'slice' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1688:74: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1692:41: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_char' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1692:41: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1692:60: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_char' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1692:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1692:75: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_char' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1692:75: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1692:85: style: Parameter 'out' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_char' is a callback function, if 'out' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1692:85: note: Parameter 'out' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1692:95: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_char' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1692:95: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1703:47: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xdelta_decode_block' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:1785:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1703:47: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1734:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1810:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1873:19: style: Variable 'dat' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1886:18: style: Variable 'dat' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1914:35: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_xdelta_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2023:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1914:35: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1949:41: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xdelta_encode_long' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1949:41: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1949:60: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xdelta_encode_long' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1949:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1950:34: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xdelta_encode_long' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1950:34: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1954:40: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xdelta_encode_int' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1954:40: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1954:59: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xdelta_encode_int' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1954:59: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1955:33: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xdelta_encode_int' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:1955:33: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:1977:19: style: Variable 'in16' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2046:39: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xrle_decode_long' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2046:39: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2046:58: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xrle_decode_long' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2046:58: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2046:73: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xrle_decode_long' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2046:73: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2046:83: style: Parameter 'out' can be declared as pointer to const. However it seems that 'cram_xrle_decode_long' is a callback function, if 'out' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2046:83: note: Parameter 'out' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2046:93: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xrle_decode_long' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2046:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2051:38: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xrle_decode_int' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2051:38: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2051:57: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xrle_decode_int' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2051:57: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2051:72: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xrle_decode_int' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2051:72: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2051:82: style: Parameter 'out' can be declared as pointer to const. However it seems that 'cram_xrle_decode_int' is a callback function, if 'out' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2051:82: note: Parameter 'out' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2051:92: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xrle_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2051:92: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2108:93: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_xrle_decode_char' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2185:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2108:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2119:5: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2187:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2286:35: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_xrle_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2409:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2286:35: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2341:39: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xrle_encode_long' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2341:39: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2341:58: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xrle_encode_long' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2341:58: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2342:34: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xrle_encode_long' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2342:34: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2347:38: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_xrle_encode_int' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2347:38: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2347:57: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_xrle_encode_int' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2347:57: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2348:33: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_xrle_encode_int' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2348:33: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2434:90: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_subexp_decode' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2507:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2434:90: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2528:89: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_gamma_decode' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2582:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2528:89: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2623:42: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2623:42: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2623:61: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2623:61: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2624:42: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2624:42: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2624:52: style: Parameter 'out' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'out' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2624:52: note: Parameter 'out' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2624:62: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2624:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2629:63: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_char0' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4072:26: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2629:63: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2643:62: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_char' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4074:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2643:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2678:62: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_int0' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4076:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2678:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2691:61: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4078:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2691:61: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2728:63: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_long0' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4080:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2728:63: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2741:62: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_long' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4082:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2741:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2820:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2952:62: style: Condition 'option==E_BYTE' is always false [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2971:43: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_huffman_encode_char0' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4073:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2971:43: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2971:62: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_huffman_encode_char0' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4073:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2971:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2972:37: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_huffman_encode_char0' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4073:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:2972:37: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2979:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:2983:17: style: Condition 'sym>=-1' is always true [knownConditionTrueFalse] htslib-1.22.1/cram/cram_codecs.c:2982:19: note: Assignment 'sym=*syms++', assigned value is greater than -1 htslib-1.22.1/cram/cram_codecs.c:2983:17: note: Condition 'sym>=-1' is always true 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3007:42: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_huffman_encode_int0' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4077:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3007:42: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3007:61: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_huffman_encode_int0' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4077:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3007:61: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3008:36: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_huffman_encode_int0' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4077:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3008:36: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3015:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3044:43: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_huffman_encode_long0' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4081:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3044:43: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3044:62: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_huffman_encode_long0' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4081:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3044:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3045:37: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_huffman_encode_long0' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4081:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3045:37: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3052:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3094:67: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_huffman_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4062:20: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3094:67: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3108:33: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] htslib-1.22.1/cram/cram_codecs.c:3107:23: note: Assuming allocation function fails htslib-1.22.1/cram/cram_codecs.c:3107:23: note: Assignment 'tmp=malloc(6*c->u.e_huffman.nvals+16)', assigned value is 0 htslib-1.22.1/cram/cram_codecs.c:3108:33: note: Null pointer addition 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3196:17: style: Local variable 'k' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_codecs.c:3165:44: note: Shadowed declaration htslib-1.22.1/cram/cram_codecs.c:3196:17: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3484:44: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_byte_array_len_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4133:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3484:44: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3563:76: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_byte_array_stop_decode_char' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:3682:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3563:76: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3566:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3610:25: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3632:24: style: Variable 'cp_start' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3713:39: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_byte_array_stop_encode' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4154:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3713:39: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:3729:45: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_byte_array_stop_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4153:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:3729:45: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:390:62: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_external_decode_char' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4028:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:390:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:393:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:410:70: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_external_decode_block' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4030:31: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:410:70: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:413:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:439:62: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_external_decode_size' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:504:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:439:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:440:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:450:68: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_external_get_block' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:505:20: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:450:68: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:548:37: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_external_encode_char' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4031:25: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:548:37: note: Parameter 'in' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:562:68: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_external_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4023:20: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:562:68: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:589:45: style: Parameter 'dat' can be declared as pointer to const. However it seems that 'cram_external_encode_init' is a callback function, if 'dat' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:3877:5: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:589:45: note: Parameter 'dat' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:737:60: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_varint_decode_size' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:793:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:737:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:738:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:748:66: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_varint_get_block' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:794:20: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:748:66: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:801:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:813:15: style: Variable 'i32' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:820:14: style: Variable 'i32' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:827:15: style: Variable 'i64' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:834:14: style: Variable 'i64' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_codecs.c:845:66: style: Parameter 'prefix' can be declared as pointer to const. However it seems that 'cram_varint_encode_store' is a callback function, if 'prefix' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:4040:20: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:845:66: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:869:49: style: Parameter 'st' can be declared as pointer to const. However it seems that 'cram_varint_encode_init' is a callback function, if 'st' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:3894:5: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:869:49: note: Parameter 'st' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:872:43: style: Parameter 'dat' can be declared as pointer to const. However it seems that 'cram_varint_encode_init' is a callback function, if 'dat' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:3894:5: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:872:43: note: Parameter 'dat' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:924:60: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_const_decode_byte' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:982:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:924:60: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:934:59: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_const_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:984:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:934:59: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:945:60: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_const_decode_long' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:986:21: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:945:60: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:960:40: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_const_decode_size' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:960:40: note: Parameter 'slice' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:960:59: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_const_decode_size' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here htslib-1.22.1/cram/cram_codecs.c:960:59: note: Parameter 'c' can be declared as pointer to const 2.19.0 htslib-1.22.1/cram/cram_codecs.c:995:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_codecs.h:230:52: style: Parameter 'blk' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1229:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1419:34: style: Variable 'dlen' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1505:38: style: Local variable 'r' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_decode.c:1099:26: note: Shadowed declaration htslib-1.22.1/cram/cram_decode.c:1505:38: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_decode.c:1512:29: style: Variable 'md_dist' is reassigned a value before the old one has been used. [redundantAssignment] htslib-1.22.1/cram/cram_decode.c:1499:37: note: md_dist is assigned htslib-1.22.1/cram/cram_decode.c:1512:29: note: md_dist is overwritten 2.19.0 htslib-1.22.1/cram/cram_decode.c:1708:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1713:35: style: Variable 'refp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:175:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1814:28: style: Variable 'orig_aux_p' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1888:58: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1916:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_decode.c:1903:19: note: Shadowed declaration htslib-1.22.1/cram/cram_decode.c:1916:21: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_decode.c:1985:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_decode.c:1957:19: note: Shadowed declaration htslib-1.22.1/cram/cram_decode.c:1985:21: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_decode.c:1990:66: warning: Expression 'TN[2]=='*'?-1:1' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] 2.19.0 htslib-1.22.1/cram/cram_decode.c:1992:66: warning: Expression 'TN[2]=='*'?-1:1' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] 2.19.0 htslib-1.22.1/cram/cram_decode.c:2233:39: style: Parameter 'md5' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:2250:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:2275:34: style:inconclusive: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. [funcArgNamesDifferent] htslib-1.22.1/cram/cram_decode.h:114:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. htslib-1.22.1/cram/cram_decode.c:2275:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. 2.19.0 htslib-1.22.1/cram/cram_decode.c:2310:19: style: The if condition is the same as the previous if condition [duplicateCondition] htslib-1.22.1/cram/cram_decode.c:2309:19: note: First condition htslib-1.22.1/cram/cram_decode.c:2310:19: note: Second condition 2.19.0 htslib-1.22.1/cram/cram_decode.c:2442:25: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:2876:31: style: Local variable 'c' shadows outer argument [shadowArgument] htslib-1.22.1/cram/cram_decode.c:2274:52: note: Shadowed declaration htslib-1.22.1/cram/cram_decode.c:2876:31: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_decode.c:2979:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_decode.c:3014:41: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:3020:11: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:3020:17: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:552:41: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:875:55: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:881:21: style: Local variable 'c' shadows outer argument [shadowArgument] htslib-1.22.1/cram/cram_decode.c:875:72: note: Shadowed declaration htslib-1.22.1/cram/cram_decode.c:881:21: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_decode.c:926:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_decode.c:938:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1246:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_encode.c:125:13: style: Local variable 'r' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:88:16: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:125:13: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:1304:14: style: Variable 'TC' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1340:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1401:20: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1433:36: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1477:29: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1477:58: style: Parameter 'skip' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1550:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1649:13: style: Local variable 'ret' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:1646:9: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:1649:13: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:1657:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1661:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1674:28: style: Variable 'L16' can be declared as const array [constVariable] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1681:25: style: The comparison 'ret < 0' is always false. [knownConditionTrueFalse] htslib-1.22.1/cram/cram_encode.c:1646:15: note: 'ret' is assigned value '0' here. htslib-1.22.1/cram/cram_encode.c:1681:25: note: The comparison 'ret < 0' is always false. 2.19.0 htslib-1.22.1/cram/cram_encode.c:1789:21: style: Variable 'm5tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1794:11: style: Variable 'ref' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:1872:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:2552:59: style: Parameter 'f' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:2607:51: style: Parameter 'base' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:2661:54: style: Parameter 'base' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:2870:13: style: Local variable 'key' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:2773:11: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:2870:13: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:2907:25: style: Local variable 'c' shadows outer argument [shadowArgument] htslib-1.22.1/cram/cram_encode.c:2762:55: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:2907:25: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:3252:27: style: The statement 'if (c->ref_seq_id!=s->hdr->ref_seq_id) c->ref_seq_id=s->hdr->ref_seq_id' is logically equivalent to 'c->ref_seq_id=s->hdr->ref_seq_id'. [duplicateConditionalAssign] htslib-1.22.1/cram/cram_encode.c:3253:28: note: Assignment 'c->ref_seq_id=s->hdr->ref_seq_id' htslib-1.22.1/cram/cram_encode.c:3252:27: note: Condition 'c->ref_seq_id!=s->hdr->ref_seq_id' is redundant 2.19.0 htslib-1.22.1/cram/cram_encode.c:3491:27: style: Variable 'sp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:3492:27: style: Variable 'rp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:3493:27: style: Variable 'qp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:3716:20: style: Variable 'brg' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:3726:24: style: Local variable 'brg' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:3716:20: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:3726:24: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:3726:24: style: Variable 'brg' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:3750:19: style: Variable 'from' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:3757:25: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:3363:9: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:3757:25: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:3759:39: style: Local variable 'c' shadows outer argument [shadowArgument] htslib-1.22.1/cram/cram_encode.c:3359:58: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:3759:39: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:3785:19: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:4126:25: style: Condition 'c->refs_used' is always true [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/cram/cram_encode.c:573:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:659:22: style: Local variable 'i32' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:579:13: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:659:22: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:70:26: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:803:61: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_encode.c:828:11: style: The if condition is the same as the previous if condition [duplicateCondition] htslib-1.22.1/cram/cram_encode.c:818:11: note: First condition htslib-1.22.1/cram/cram_encode.c:828:11: note: Second condition 2.19.0 htslib-1.22.1/cram/cram_encode.c:851:13: style: Variable 'methodF' is reassigned a value before the old one has been used. [redundantAssignment] htslib-1.22.1/cram/cram_encode.c:843:17: note: methodF is assigned htslib-1.22.1/cram/cram_encode.c:851:13: note: methodF is overwritten 2.19.0 htslib-1.22.1/cram/cram_encode.c:955:13: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:804:28: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:955:13: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_encode.c:973:13: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_encode.c:804:28: note: Shadowed declaration htslib-1.22.1/cram/cram_encode.c:973:13: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_external.c:104:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:120:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:124:48: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:500:61: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:504:59: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:508:54: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:525:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:526:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:527:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:528:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:529:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:530:58: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:533:64: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:554:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:568:50: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:58:40: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:619:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RANS_ORDER_X32 [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_external.c:619:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:61:34: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:620:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:621:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:622:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:623:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:624:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:632:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:633:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:634:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:635:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:636:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/cram/cram_external.c:64:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:65:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:67:32: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:725:61: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:75:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:803:21: style: Variable 'cd' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:84:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:92:56: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:936:49: style: Parameter 'out_rg' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:96:54: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_external.c:976:8: style: Redundant initialization for 'op'. The initialized value is overwritten before it is read. [redundantInitialization] htslib-1.22.1/cram/cram_external.c:967:14: note: op is initialized htslib-1.22.1/cram/cram_external.c:976:8: note: op is overwritten 2.19.0 htslib-1.22.1/cram/cram_index.c:1023:17: style: Variable 'ci' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_index.c:405:42: style:inconclusive: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. [funcArgNamesDifferent] htslib-1.22.1/cram/cram_index.h:54:81: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. htslib-1.22.1/cram/cram_index.c:405:42: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. 2.19.0 htslib-1.22.1/cram/cram_index.c:478:30: style: Condition 'from->e[k].starte[k].start>=pos' is not redundant htslib-1.22.1/cram/cram_index.c:478:30: note: Condition 'from->e[k].startcram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment] htslib-1.22.1/cram/cram_io.c:5244:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned htslib-1.22.1/cram/cram_io.c:5245:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten 2.19.0 htslib-1.22.1/cram/cram_io.c:5246:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment] htslib-1.22.1/cram/cram_io.c:5245:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned htslib-1.22.1/cram/cram_io.c:5246:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten 2.19.0 htslib-1.22.1/cram/cram_io.c:5247:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment] htslib-1.22.1/cram/cram_io.c:5246:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned htslib-1.22.1/cram/cram_io.c:5247:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten 2.19.0 htslib-1.22.1/cram/cram_io.c:5296:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_io.c:5669:23: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_io.c:5703:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_io.c:5811:21: style: Variable 'r' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/cram/cram_io.c:5998:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/cram/cram_io.h:646:49: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/cram/cram_stats.c:168:13: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/cram/cram_stats.c:135:16: note: Shadowed declaration htslib-1.22.1/cram/cram_stats.c:168:13: note: Shadow variable 2.19.0 htslib-1.22.1/cram/cram_structs.h:67:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 htslib-1.22.1/cram/cram_structs.h:686:1: warning: Null pointer dereference: empty [ctunullpointer] htslib-1.22.1/cram/cram_io.c:2808:13: note: Assuming that condition '!h->hrecs->ref[i].name' is not redundant htslib-1.22.1/cram/cram_io.c:2800:13: note: Calling function kh_get_refs, 2nd argument is null htslib-1.22.1/cram/cram_structs.h:686:1: note: Dereferencing argument empty that is null 2.19.0 htslib-1.22.1/header.c:1080:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/header.c:1114:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/header.c:1187:22: style: Variable 'first' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1217:34: style:inconclusive: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:445:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1217:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1219:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/header.c:1224:36: style:inconclusive: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:458:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1224:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1231:35: style:inconclusive: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:465:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1231:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1296:34: style:inconclusive: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:483:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1296:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1331:33: style:inconclusive: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:499:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1331:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1345:47: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/header.c:1364:37: style:inconclusive: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:518:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1364:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1376:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1388:38: style:inconclusive: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:536:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1388:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1400:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1422:39: style:inconclusive: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:561:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1422:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:143:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1461:40: style:inconclusive: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:573:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1461:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1510:11: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1510:17: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1512:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1548:36: style:inconclusive: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:600:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1548:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1653:38: style:inconclusive: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:617:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1653:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1709:37: style:inconclusive: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:657:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1709:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1709:81: style:inconclusive: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:657:80: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. htslib-1.22.1/header.c:1709:81: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. 2.19.0 htslib-1.22.1/header.c:1711:15: style: Variable 'rh' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1739:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1755:22: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1760:17: style: Variable 'head' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/header.c:1781:36: style:inconclusive: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:666:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1781:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1783:33: style: Variable 'itr_ty' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1921:36: style:inconclusive: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:707:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1921:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1941:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1946:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/header.c:1953:37: style:inconclusive: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:725:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1953:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:1972:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:1977:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/header.c:1984:38: style:inconclusive: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:736:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:1984:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:201:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/header.c:2031:33: style:inconclusive: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:749:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:2031:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:2200:38: style:inconclusive: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:792:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:2200:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:2251:31: style:inconclusive: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:810:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:2251:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:2323:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/header.c:2339:65: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/header.c:2356:34: style:inconclusive: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:830:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/header.c:2356:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/header.c:2508:27: style: Variable 't2' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:2550:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:2583:15: style: Variable 'k' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:2583:19: style: Variable 'v' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:2681:25: style: Variable 'sn_tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:2801:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:321:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:414:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:41:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 htslib-1.22.1/header.c:597:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:597:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:634:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:634:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:66:64: style: Parameter 'type_list' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/header.c:682:43: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/header.c:711:14: style: Variable 'hrecs->first_line' is assigned an expression that holds the same value. [redundantAssignment] htslib-1.22.1/header.c:710:27: note: Assuming that condition 'hrecs->first_line==type_found' is not redundant htslib-1.22.1/header.c:710:27: note: Assuming that condition 'hrecs->first_line==type_found' is not redundant htslib-1.22.1/header.c:711:14: note: Variable 'hrecs->first_line' is assigned an expression that holds the same value. 2.19.0 htslib-1.22.1/header.c:741:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/header.c:743:10: style: Variable 'c' can be declared as const array [constVariable] 2.19.0 htslib-1.22.1/header.c:745:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/header.c:777:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SSIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:1171:46: style: Same expression on both sides of '||'. [duplicateExpression] 2.19.0 htslib-1.22.1/hts.c:1172:41: style: Condition 'strcmp(o->arg,"store_md")==0' is always false [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/hts.c:1175:46: style: Same expression on both sides of '||'. [duplicateExpression] 2.19.0 htslib-1.22.1/hts.c:1176:41: style: Condition 'strcmp(o->arg,"store_nm")==0' is always false [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/hts.c:1240:14: style: Variable 'last' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:1290:35: style:inconclusive: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:452:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. htslib-1.22.1/hts.c:1290:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. 2.19.0 htslib-1.22.1/hts.c:1296:21: style: Redundant condition: The condition '*str' is redundant since '*str == ','' is sufficient. [redundantCondition] 2.19.0 htslib-1.22.1/hts.c:1327:33: style:inconclusive: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:438:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. htslib-1.22.1/hts.c:1327:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. 2.19.0 htslib-1.22.1/hts.c:136:43: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/hts.c:138:38: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/hts.c:140:39: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/hts.c:142:46: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/hts.c:1440:48: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/hts.c:144:41: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/hts.c:1453:27: style:inconclusive: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:630:34: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. htslib-1.22.1/hts.c:1453:27: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. 2.19.0 htslib-1.22.1/hts.c:1458:34: style: Variable 'opts' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:146:40: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 htslib-1.22.1/hts.c:1489:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:152:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_CC [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:1633:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:1867:15: style: Variable 'expr' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:1983:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2031:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2048:33: style:inconclusive: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:697:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. htslib-1.22.1/hts.c:2048:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. 2.19.0 htslib-1.22.1/hts.c:2065:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2126:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2216:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2217:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2225:1: error: Null pointer dereference: empty [ctunullpointer] htslib-1.22.1/hts.c:2448:9: note: Calling function kh_get_bin, 2nd argument is null htslib-1.22.1/hts.c:2225:1: note: Dereferencing argument empty that is null 2.19.0 htslib-1.22.1/hts.c:2488:36: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/hts.c:2504:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2533:64: style: Condition 'tid<0' is always false [knownConditionTrueFalse] htslib-1.22.1/hts.c:2533:52: note: Assuming that condition 'idx->z.last_tid>=0' is not redundant htslib-1.22.1/hts.c:2533:25: note: Assuming that condition 'idx->z.last_tid!=tid' is not redundant htslib-1.22.1/hts.c:2533:64: note: Condition 'tid<0' is always false 2.19.0 htslib-1.22.1/hts.c:2664:28: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/hts.c:2673:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/hts.c:2673:18: note: Calling function 'ed_is_big' returns 0 htslib-1.22.1/hts.c:2673:18: note: Condition 'ed_is_big()' is always false 2.19.0 htslib-1.22.1/hts.c:2679:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/hts.c:2679:18: note: Calling function 'ed_is_big' returns 0 htslib-1.22.1/hts.c:2679:18: note: Condition 'ed_is_big()' is always false 2.19.0 htslib-1.22.1/hts.c:2685:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] htslib-1.22.1/htslib/hts.h:1559:15: note: Assignment 'one=1', assigned value is 1 htslib-1.22.1/hts.c:2685:18: note: Calling function 'ed_is_big' returns 0 htslib-1.22.1/hts.c:2685:18: note: Condition 'ed_is_big()' is always false 2.19.0 htslib-1.22.1/hts.c:2733:17: style: Variable 'lidx' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:2741:29: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:2778:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2830:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2850:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2905:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:2913:17: style: Local variable 'j' shadows outer variable [shadowVariable] htslib-1.22.1/hts.c:2884:13: note: Shadowed declaration htslib-1.22.1/hts.c:2913:17: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:2918:22: style: Condition 'l->n<0' is always false [knownConditionTrueFalse] htslib-1.22.1/hts.c:2917:20: note: Assignment 'l->n=x', assigned value is greater than -1 htslib-1.22.1/hts.c:2918:22: note: Condition 'l->n<0' is always false 2.19.0 htslib-1.22.1/hts.c:2956:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:3018:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:3034:38: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/hts.c:3052:17: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:3097:112: style: Parameter 'bidx' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/hts.c:3155:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:3245:21: style: Local variable 'bin' shadows outer variable [shadowVariable] htslib-1.22.1/hts.c:3238:19: note: Shadowed declaration htslib-1.22.1/hts.c:3245:21: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:3259:13: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:3312:20: style: Variable 'reg1' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:3313:20: style: Variable 'reg2' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:3385:23: style: Variable 'unmapped' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/hts.c:3390:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:3397:22: style: Local variable 'off' shadows outer variable [shadowVariable] htslib-1.22.1/hts.c:3379:23: note: Shadowed declaration htslib-1.22.1/hts.c:3397:22: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:3604:31: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:3703:19: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:3887:47: style: Redundant condition: !(flags&1). 'flags&1 || (!(flags&1) && *s!=',')' is equivalent to 'flags&1 || *s!=','' [redundantCondition] 2.19.0 htslib-1.22.1/hts.c:4071:18: style: Condition '*beg!=-1' is always false [knownConditionTrueFalse] htslib-1.22.1/hts.c:4069:29: note: Calling function 'hts_parse_decimal' returns !<=-1 htslib-1.22.1/hts.c:4069:55: note: Assignment '*beg=hts_parse_decimal(colon+1,&hyphen,flags)-1', assigned value is greater than -2 htslib-1.22.1/hts.c:4070:14: note: Assuming that condition '*beg<0' is not redundant htslib-1.22.1/hts.c:4071:18: note: Condition '*beg!=-1' is always false 2.19.0 htslib-1.22.1/hts.c:4110:41: style:inconclusive: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:1181:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. htslib-1.22.1/hts.c:4110:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. 2.19.0 htslib-1.22.1/hts.c:4130:39: style:inconclusive: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:1191:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. htslib-1.22.1/hts.c:4130:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. 2.19.0 htslib-1.22.1/hts.c:4229:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:4263:53: style: Condition 'iter->end>beg' is always true [knownConditionTrueFalse] htslib-1.22.1/hts.c:4261:41: note: Assuming that condition 'beg>=iter->end' is not redundant htslib-1.22.1/hts.c:4263:53: note: Condition 'iter->end>beg' is always true 2.19.0 htslib-1.22.1/hts.c:4280:20: style: Variable 'found_reg' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/hts.c:4369:32: style: Variable 'next_range' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/hts.c:4375:36: style: Local variable 'r' shadows outer argument [shadowArgument] htslib-1.22.1/hts.c:4275:60: note: Shadowed declaration htslib-1.22.1/hts.c:4375:36: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:4400:32: style: Condition 'iter->in_off' is always true [knownConditionTrueFalse] htslib-1.22.1/hts.c:4367:25: note: Assuming that condition 'iter->i>=iter->n_off' is not redundant htslib-1.22.1/hts.c:4400:32: note: Condition 'iter->in_off' is always true 2.19.0 htslib-1.22.1/hts.c:4430:40: style: Local variable 'r' shadows outer argument [shadowArgument] htslib-1.22.1/hts.c:4275:60: note: Shadowed declaration htslib-1.22.1/hts.c:4430:40: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:4446:33: style: Local variable 'tid' shadows outer variable [shadowVariable] htslib-1.22.1/hts.c:4278:14: note: Shadowed declaration htslib-1.22.1/hts.c:4446:33: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:4447:37: style: Local variable 'end' shadows outer variable [shadowVariable] htslib-1.22.1/hts.c:4279:20: note: Shadowed declaration htslib-1.22.1/hts.c:4447:37: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:4524:50: error: Uninitialized variables: &key.reg, &key.intervals, &key.count, &key.min_beg, &key.max_end [uninitvar] 2.19.0 htslib-1.22.1/hts.c:4627:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:4883:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:4969:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:5005:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:5066:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:5142:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:551:30: style:inconclusive: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:545:37: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. htslib-1.22.1/hts.c:551:30: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. 2.19.0 htslib-1.22.1/hts.c:556:31: style:inconclusive: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent] htslib-1.22.1/htslib/hts.h:562:38: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. htslib-1.22.1/hts.c:556:31: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. 2.19.0 htslib-1.22.1/hts.c:627:15: style: Local variable 's' shadows outer variable [shadowVariable] htslib-1.22.1/hts.c:559:19: note: Shadowed declaration htslib-1.22.1/hts.c:627:15: note: Shadow variable 2.19.0 htslib-1.22.1/hts.c:86:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_VERSION_TEXT [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/hts.c:968:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/htsfile.c:116:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/htsfile.c:155:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/htsfile.c:257:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/htsfile.c:51:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/htsfile.c:72:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/htslib/bgzf.h:156:16: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/bgzf.h:157:16: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/bgzf.h:188:16: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/hts.h:1560:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast] 2.19.0 htslib-1.22.1/htslib/hts.h:1568:32: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/hts.h:1568:6: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/hts.h:1578:32: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/hts.h:1578:6: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/hts.h:1589:32: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/hts.h:1589:6: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/kbitset.h:106:8: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/kbitset.h:82:3: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash.h:449:10: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory] htslib-1.22.1/test/sam.c:1214:5: note: Assuming allocation function fails htslib-1.22.1/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0 htslib-1.22.1/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0 htslib-1.22.1/htslib/khash.h:449:10: note: Null pointer dereference 2.19.0 htslib-1.22.1/htslib/khash.h:449:13: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] htslib-1.22.1/test/sam.c:1214:5: note: Assuming allocation function fails htslib-1.22.1/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0 htslib-1.22.1/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0 htslib-1.22.1/htslib/khash.h:449:13: note: Null pointer addition 2.19.0 htslib-1.22.1/htslib/khash.h:449:38: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory] htslib-1.22.1/test/sam.c:1214:5: note: Assuming allocation function fails htslib-1.22.1/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0 htslib-1.22.1/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0 htslib-1.22.1/htslib/khash.h:449:38: note: Null pointer dereference 2.19.0 htslib-1.22.1/htslib/khash.h:470:64: performance: Function parameter 'ks' should be passed by const reference. [passedByValue] 2.19.0 htslib-1.22.1/htslib/khash.h:484:66: performance: Function parameter 'ks' should be passed by const reference. [passedByValue] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:100:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:118:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:131:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:30:1: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:46:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:55:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:59:37: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:68:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/khash_str2int.h:80:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/kstring.h:165:12: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/kstring.h:411:14: style: The scope of the variable 'm' can be reduced. [variableScope] 2.19.0 htslib-1.22.1/htslib/sam.h:1470:18: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/sam.h:1478:21: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/sam.h:1566:29: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/sam.h:1574:30: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/sam.h:1628:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/htslib/sam.h:1699:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] head htslib-1.22.1/htslib/sam.h:259:25: error: syntax error [syntaxError] 2.19.0 htslib-1.22.1/htslib/sam.h:966:50: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/htslib/vcf.h:1122:36: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1532:22: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1540:18: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1572:18: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1619:14: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1622:14: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1625:14: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1628:14: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/htslib/vcf.h:1660:14: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/realn.c:111:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/realn.c:112:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/realn.c:205:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/realn.c:216:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/realn.c:41:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/realn.c:42:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/realn.c:43:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/realn.c:48:27: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/realn.c:58:51: style: Condition 'qual[z]>=13' is always true [knownConditionTrueFalse] htslib-1.22.1/realn.c:56:53: note: Assuming that condition 'qual[z]>=13' is not redundant htslib-1.22.1/realn.c:58:51: note: Condition 'qual[z]>=13' is always true 2.19.0 htslib-1.22.1/realn.c:73:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/realn.c:77:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/realn.c:94:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:1100:32: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] 2.19.0 htslib-1.22.1/sam.c:1123:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:116:33: style:inconclusive: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:385:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. htslib-1.22.1/sam.c:116:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 htslib-1.22.1/sam.c:1207:14: style: Variable 'hb' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:1217:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:1307:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:1435:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:1610:17: style: Variable 's' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:1635:11: style: Variable 'fd' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:1894:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:2070:19: style: Variable 'tab' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:2100:25: style: Local variable 'absent' shadows outer variable [shadowVariable] htslib-1.22.1/sam.c:2065:20: note: Shadowed declaration htslib-1.22.1/sam.c:2100:25: note: Shadow variable 2.19.0 htslib-1.22.1/sam.c:2196:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:2227:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:2256:15: style: Variable 'text' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:2330:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:2340:18: style: Variable 'tmp' can be declared as const array [constVariable] 2.19.0 htslib-1.22.1/sam.c:2362:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:2413:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/sam.c:2439:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:258:17: style: Condition 'bufsizel_text' is always false [knownConditionTrueFalse] htslib-1.22.1/sam.c:257:13: note: bufsize is assigned 'h->l_text+1' here. htslib-1.22.1/sam.c:258:17: note: Condition 'bufsizel_text' is always false 2.19.0 htslib-1.22.1/sam.c:2667:15: style: Variable 'r' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:2740:43: style: Parameter 'tag_whitelist' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/sam.c:2744:23: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:2845:19: style: Local variable 'end' shadows outer argument [shadowArgument] htslib-1.22.1/sam.c:2739:48: note: Shadowed declaration htslib-1.22.1/sam.c:2845:19: note: Shadow variable 2.19.0 htslib-1.22.1/sam.c:2921:22: style: Variable 'q' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:2955:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:2972:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:3022:43: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/sam.c:2922:9: note: Shadowed declaration htslib-1.22.1/sam.c:3022:43: note: Shadow variable 2.19.0 htslib-1.22.1/sam.c:3357:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EIO [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:3454:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:347:11: style: Variable 'text' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:3528:34: style: Parameter 'arg' can be declared as pointer to const. However it seems that 'sam_parse_eof' is a callback function, if 'arg' is declared with const you might also need to cast function pointer(s). [constParameterCallback] htslib-1.22.1/sam.c:3665:42: note: You might need to cast the function pointer here htslib-1.22.1/sam.c:3528:34: note: Parameter 'arg' can be declared as pointer to const 2.19.0 htslib-1.22.1/sam.c:3609:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:3617:19: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:3618:19: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:3633:33: warning: Invalid test for overflow 'l->alloc>=l->alloc-line_frag'; signed integer overflow is undefined behavior. Some mainstream compilers removes handling of overflows when optimising the code and change the code to 'line_frag>=0'. [invalidTestForOverflow] 2.19.0 htslib-1.22.1/sam.c:3721:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:3872:14: style: Variable 'fp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:3885:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:396:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4066:15: style: Variable 'bc' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4108:18: error: Dereferencing 's' after it is deallocated / released [deallocuse] 2.19.0 htslib-1.22.1/sam.c:4114:11: style: Variable 'name' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4230:13: style: Condition 'ret>=0' is always true [knownConditionTrueFalse] htslib-1.22.1/sam.c:4194:13: note: Assuming that condition 'ret<0' is not redundant htslib-1.22.1/sam.c:4230:13: note: Condition 'ret>=0' is always true 2.19.0 htslib-1.22.1/sam.c:4245:57: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/sam.c:4250:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4285:17: style: Local variable 'ret' shadows outer variable [shadowVariable] htslib-1.22.1/sam.c:4271:9: note: Shadowed declaration htslib-1.22.1/sam.c:4285:17: note: Shadow variable 2.19.0 htslib-1.22.1/sam.c:4287:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:438:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4400:26: style: Variable 'x' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4411:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4440:14: style: Variable 's' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4440:18: style: Variable 'end' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4455:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4471:18: style: Local variable 's' shadows outer variable [shadowVariable] htslib-1.22.1/sam.c:4440:14: note: Shadowed declaration htslib-1.22.1/sam.c:4471:18: note: Shadow variable 2.19.0 htslib-1.22.1/sam.c:4510:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4535:15: warning: Either the condition 'x' is redundant or there is possible null pointer dereference: x. [nullPointerRedundantCheck] htslib-1.22.1/sam.c:4539:9: note: Assuming that condition 'x' is not redundant htslib-1.22.1/sam.c:4535:15: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:4535:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4766:22: style: Variable 'x' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4788:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4859:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4902:14: style: Variable 'end' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4903:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4912:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4928:22: style: Variable 'e' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:4941:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4948:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4958:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4976:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:4978:39: style: Variable 'e' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:5028:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5097:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5125:62: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/sam.c:5132:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5192:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5218:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5227:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5234:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5244:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5254:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5296:11: style: Variable 'opts' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:5354:50: style: Condition 'strncmp(format,"fa",format_len)==0' is always false [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/sam.c:5495:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:5496:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:556:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:5601:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:5660:25: style: Local variable 'j' shadows outer variable [shadowVariable] htslib-1.22.1/sam.c:5600:9: note: Shadowed declaration htslib-1.22.1/sam.c:5660:25: note: Shadow variable 2.19.0 htslib-1.22.1/sam.c:5749:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:5748:29: note: Assuming allocation function fails htslib-1.22.1/sam.c:5748:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 htslib-1.22.1/sam.c:5749:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:5750:18: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:5748:29: note: Assuming allocation function fails htslib-1.22.1/sam.c:5748:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 htslib-1.22.1/sam.c:5750:18: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:5750:40: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:5748:29: note: Assuming allocation function fails htslib-1.22.1/sam.c:5748:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 htslib-1.22.1/sam.c:5750:40: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:5750:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:5748:29: note: Assuming allocation function fails htslib-1.22.1/sam.c:5748:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 htslib-1.22.1/sam.c:5750:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:5751:21: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:5748:29: note: Assuming allocation function fails htslib-1.22.1/sam.c:5748:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 htslib-1.22.1/sam.c:5751:21: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:5751:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:5748:29: note: Assuming allocation function fails htslib-1.22.1/sam.c:5748:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 htslib-1.22.1/sam.c:5751:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:5752:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:5748:29: note: Assuming allocation function fails htslib-1.22.1/sam.c:5748:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 htslib-1.22.1/sam.c:5752:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:5892:14: style: Variable 'a_seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:5892:40: style: Variable 'b_seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:5896:29: style: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value. [duplicateExpression] htslib-1.22.1/sam.c:5894:31: note: 'iref' is assigned value 'b->core.pos' here. htslib-1.22.1/sam.c:5896:29: note: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value. 2.19.0 htslib-1.22.1/sam.c:6113:39: style: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true [knownConditionTrueFalse] htslib-1.22.1/sam.c:6113:39: note: Calling function 'resolve_cigar2' returns 1 htslib-1.22.1/sam.c:6113:39: note: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true 2.19.0 htslib-1.22.1/sam.c:61:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 htslib-1.22.1/sam.c:6291:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6291:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6292:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6292:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6293:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6293:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6294:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6294:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6295:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6295:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6296:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6296:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6297:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6297:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6298:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6298:5: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6300:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6300:9: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6301:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6301:24: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6301:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6301:9: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6302:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6302:24: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:6302:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] htslib-1.22.1/sam.c:6290:30: note: Assuming allocation function fails htslib-1.22.1/sam.c:6290:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 htslib-1.22.1/sam.c:6302:9: note: Null pointer dereference 2.19.0 htslib-1.22.1/sam.c:689:14: style: Variable 'CG' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam.c:690:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:863:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam.c:955:27: style:inconclusive: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. [funcArgNamesDifferent] htslib-1.22.1/htslib/sam.h:1115:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. htslib-1.22.1/sam.c:955:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. 2.19.0 htslib-1.22.1/sam.c:962:17: style: Condition 'new_len<1' is always false [knownConditionTrueFalse] htslib-1.22.1/sam.c:961:36: note: Assignment 'new_len=strlen(qname)+1', assigned value is greater than 0 htslib-1.22.1/sam.c:962:17: note: Condition 'new_len<1' is always false 2.19.0 htslib-1.22.1/sam_internal.h:57:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/sam_internal.h:72:49: style: Parameter 'nib' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/sam_mods.c:206:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam_mods.c:248:14: style: Variable 'mi' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam_mods.c:264:14: style: Variable 'ml_end' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam_mods.c:274:18: style: Variable 'implicit' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/sam_mods.c:482:15: style: Variable 'MMptr' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/sam_mods.c:601:13: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/sam_mods.c:559:35: note: Shadowed declaration htslib-1.22.1/sam_mods.c:601:13: note: Shadow variable 2.19.0 htslib-1.22.1/sam_mods.c:647:44: style: Parameter 'state' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/tabix.c:117:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/tabix.c:206:52: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/tabix.c:437:81: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/tabix.c:460:15: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/tabix.c:499:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/tabix.c:618:11: style: Variable 'reheader' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/tabix.c:64:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/tabix.c:657:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/tabix.c:76:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/tabix.c:784:11: style: Variable 'suffix' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/fieldarith.c:37:14: style: Variable 'aux' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/fieldarith.c:42:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/fuzz/hts_open_fuzzer.c:121:62: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/fuzz/hts_open_fuzzer.c:46:62: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/pileup.c:126:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup.c:148:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/pileup.c:196:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/pileup.c:235:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/pileup.c:81:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:102:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:103:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:140:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:151:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:152:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:157:13: style: Local variable 'n' shadows outer argument [shadowArgument] htslib-1.22.1/test/pileup_mod.c:141:47: note: Shadowed declaration htslib-1.22.1/test/pileup_mod.c:157:13: note: Shadow variable 2.19.0 htslib-1.22.1/test/pileup_mod.c:161:16: style: Variable 'n' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/test/pileup_mod.c:49:32: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:60:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:61:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/pileup_mod.c:91:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/sam.c:101:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/sam.c:1055:46: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1064:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:1068:34: warning: Either the condition '!text' is redundant or there is possible null pointer dereference: text. [nullPointerRedundantCheck] htslib-1.22.1/test/sam.c:1062:13: note: Assuming that condition '!text' is not redundant htslib-1.22.1/test/sam.c:1068:34: note: Null pointer dereference 2.19.0 htslib-1.22.1/test/sam.c:1126:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1128:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1130:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1132:73: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1139:71: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1142:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1145:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1170:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:1228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:1273:64: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1276:81: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1281:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1289:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1297:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1322:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1331:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1340:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:1558:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:1581:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:1590:37: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources] htslib-1.22.1/test/sam.c:1585:16: note: Assuming allocation function fails htslib-1.22.1/test/sam.c:1585:16: note: Assignment 'fin=fopen(filename,"rb")', assigned value is 0 htslib-1.22.1/test/sam.c:1590:37: note: Null pointer dereference 2.19.0 htslib-1.22.1/test/sam.c:1593:21: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources] htslib-1.22.1/test/sam.c:1588:17: note: Assuming allocation function fails htslib-1.22.1/test/sam.c:1588:17: note: Assignment 'fout=fopen(tmpfilename,"wb")', assigned value is 0 htslib-1.22.1/test/sam.c:1593:21: note: Null pointer dereference 2.19.0 htslib-1.22.1/test/sam.c:1596:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources] htslib-1.22.1/test/sam.c:1588:17: note: Assuming allocation function fails htslib-1.22.1/test/sam.c:1588:17: note: Assignment 'fout=fopen(tmpfilename,"wb")', assigned value is 0 htslib-1.22.1/test/sam.c:1596:12: note: Null pointer dereference 2.19.0 htslib-1.22.1/test/sam.c:1664:24: style: The comparison 'no_compression != 0' is always false. [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/test/sam.c:1665:14: style: The comparison 'gzip != 1' is always false. [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/test/sam.c:1666:14: style: The comparison 'bgzf != 2' is always false. [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/test/sam.c:1783:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2005:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2041:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2086:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2115:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2137:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2154:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2174:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2203:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2243:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:2248:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:2310:11: style: Variable 'cig' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/sam.c:2315:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:318:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:443:15: style: The if condition is the same as the previous if condition [duplicateCondition] htslib-1.22.1/test/sam.c:442:15: note: First condition htslib-1.22.1/test/sam.c:443:15: note: Second condition 2.19.0 htslib-1.22.1/test/sam.c:444:15: style: The if condition is the same as the previous if condition [duplicateCondition] htslib-1.22.1/test/sam.c:443:15: note: First condition htslib-1.22.1/test/sam.c:444:15: note: Second condition 2.19.0 htslib-1.22.1/test/sam.c:445:15: style: The if condition is the same as the previous if condition [duplicateCondition] htslib-1.22.1/test/sam.c:444:15: note: First condition htslib-1.22.1/test/sam.c:445:15: note: Second condition 2.19.0 htslib-1.22.1/test/sam.c:48:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 htslib-1.22.1/test/sam.c:48:1: warning: If memory allocation fails, then there is a possible null pointer dereference: empty [ctunullpointerOutOfMemory] htslib-1.22.1/test/sam.c:1214:5: note: Assuming allocation function fails htslib-1.22.1/test/sam.c:1214:5: note: Calling function kh_put_keep, 2nd argument is null htslib-1.22.1/test/sam.c:48:1: note: Dereferencing argument empty that is null 2.19.0 htslib-1.22.1/test/sam.c:498:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/test/sam.c:64:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:763:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:766:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:770:49: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:773:55: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:781:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:784:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:787:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:851:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:901:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:956:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:960:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:964:63: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:967:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:970:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:980:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:983:61: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 htslib-1.22.1/test/sam.c:992:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/sam.c:996:27: warning: Either the condition '!text' is redundant or there is possible null pointer dereference: text. [nullPointerRedundantCheck] htslib-1.22.1/test/sam.c:990:9: note: Assuming that condition '!text' is not redundant htslib-1.22.1/test/sam.c:996:27: note: Null pointer dereference 2.19.0 htslib-1.22.1/test/sam.c:99:39: style: Parameter 'aln' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/test-bcf_set_variant_type.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test-parse-reg.c:172:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test-parse-reg.c:51:24: style: Parameter 'reg_exp' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/test-parse-reg.c:63:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test-parse-reg.c:72:20: style: Parameter 'fn' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/test-parse-reg.c:98:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_index.c:39:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_index.c:49:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_mod.c:120:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_mod.c:173:14: style: Variable 'all_mods' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/test_nibbles.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_nibbles.c:155:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_nibbles.c:54:17: style: Local variable 'buf' shadows outer variable [shadowVariable] htslib-1.22.1/test/test_nibbles.c:76:6: note: Shadowed declaration htslib-1.22.1/test/test_nibbles.c:54:17: note: Shadow variable 2.19.0 htslib-1.22.1/test/test_nibbles.c:69:34: style: Parameter 'nib' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/test_realn.c:39:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_realn.c:45:11: style: Variable 'in_name' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/test_realn.c:46:11: style: Variable 'out_name' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/test_realn.c:47:11: style: Variable 'ref_name' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/test_realn.c:49:10: style: Variable 'modew' can be declared as const array [constVariable] 2.19.0 htslib-1.22.1/test/test_realn.c:60:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_view.c:200:29: style: Variable 'r' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/test/test_view.c:212:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_view.c:286:11: style: Variable 'out_fn' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/test/test_view.c:306:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/test_view.c:73:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/test/usepublic.cpp:61:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 htslib-1.22.1/test/usepublic.cpp:61:1: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/test/usepublic.cpp:64:1: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/test/usepublic.cpp:64:1: warning: If memory allocation fails, then there is a possible null pointer dereference: kl [nullPointerOutOfMemory] htslib-1.22.1/test/usepublic.cpp:64:1: note: Assuming allocation function fails htslib-1.22.1/test/usepublic.cpp:64:1: note: Assignment 'kl=(struct kl_intlist_t*)calloc(1,sizeof(struct kl_intlist_t))', assigned value is 0 htslib-1.22.1/test/usepublic.cpp:64:1: note: Null pointer dereference 2.19.0 htslib-1.22.1/test/usepublic.cpp:66:1: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/test/usepublic.cpp:70:1: style: C-style pointer casting [cstyleCast] 2.19.0 htslib-1.22.1/test/usepublic.cpp:70:1: style: Parameter 'f' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/test/usepublic.cpp:70:1: warning: If memory allocation fails, then there is a possible null pointer dereference: ks [nullPointerOutOfMemory] htslib-1.22.1/test/usepublic.cpp:70:1: note: Assuming allocation function fails htslib-1.22.1/test/usepublic.cpp:70:1: note: Assignment 'ks=(struct kstream_t*)calloc(1,sizeof(struct kstream_t))', assigned value is 0 htslib-1.22.1/test/usepublic.cpp:70:1: note: Null pointer dereference 2.19.0 htslib-1.22.1/test/usepublic.cpp:70:1: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory] htslib-1.22.1/test/usepublic.cpp:70:1: note: Assuming allocation function fails htslib-1.22.1/test/usepublic.cpp:70:1: note: Assignment 's=(struct kseq_t*)calloc(1,sizeof(struct kseq_t))', assigned value is 0 htslib-1.22.1/test/usepublic.cpp:70:1: note: Null pointer dereference 2.19.0 htslib-1.22.1/textutils.c:169:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/textutils.c:185:23: style: Variable 'lim' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/textutils.c:202:40: style: Parameter 'token' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/textutils.c:228:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/textutils.c:238:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/textutils.c:327:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/textutils.c:455:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/textutils.c:456:21: style: Variable 'bufend' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:1012:50: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:1053:36: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:1233:38: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:1240:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:1290:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:1338:31: style:inconclusive: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:596:35: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. htslib-1.22.1/vcf.c:1338:31: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. 2.19.0 htslib-1.22.1/vcf.c:1348:32: style:inconclusive: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:621:36: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. htslib-1.22.1/vcf.c:1348:32: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. 2.19.0 htslib-1.22.1/vcf.c:1413:31: style:inconclusive: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:599:35: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. htslib-1.22.1/vcf.c:1413:31: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. 2.19.0 htslib-1.22.1/vcf.c:1413:48: style:inconclusive: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:599:50: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. htslib-1.22.1/vcf.c:1413:48: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. 2.19.0 htslib-1.22.1/vcf.c:1445:17: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:146:26: style: Variable 'minor' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:1491:20: style: Variable 'dsize' can be declared as const array [constVariable] 2.19.0 htslib-1.22.1/vcf.c:1551:34: style:inconclusive: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:340:38: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. htslib-1.22.1/vcf.c:1551:34: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. 2.19.0 htslib-1.22.1/vcf.c:1590:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:1608:28: style:inconclusive: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:376:32: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. htslib-1.22.1/vcf.c:1608:28: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. 2.19.0 htslib-1.22.1/vcf.c:1611:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:173:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:1752:57: style: Parameter 'end' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:1808:64: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:1839:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:1903:19: style: Variable 'id_tmp' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:1990:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:2028:45: style:inconclusive: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:506:49: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. htslib-1.22.1/vcf.c:2028:45: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. 2.19.0 htslib-1.22.1/vcf.c:2038:40: style: Parameter 'line' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:2052:78: style: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false [knownConditionTrueFalse] htslib-1.22.1/vcf.c:2052:26: note: Calling function 'bcf_enc_vchar' returns 0 htslib-1.22.1/vcf.c:2052:78: note: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false 2.19.0 htslib-1.22.1/vcf.c:2074:21: style: Variable 'info' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:2094:11: style: Variable 'shared_ori' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:2196:24: style: Variable 'fmt' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:2270:24: style:inconclusive: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:452:28: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. htslib-1.22.1/vcf.c:2270:24: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. 2.19.0 htslib-1.22.1/vcf.c:2347:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:2382:23: style: Variable 'tab' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:2418:25: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:2464:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:250:35: style:inconclusive: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:571:39: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. htslib-1.22.1/vcf.c:250:35: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. 2.19.0 htslib-1.22.1/vcf.c:250:50: style:inconclusive: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:571:56: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. htslib-1.22.1/vcf.c:250:50: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. 2.19.0 htslib-1.22.1/vcf.c:2527:56: style:inconclusive: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:646:60: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. htslib-1.22.1/vcf.c:2527:56: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. 2.19.0 htslib-1.22.1/vcf.c:2547:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:2594:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:2596:17: style: Variable 'max' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/vcf.c:2596:34: style: Variable 'min' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/vcf.c:2722:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:2810:19: style: Variable 'p_end' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:2897:47: style: Parameter 's' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:2963:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable info [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:2970:45: style: Parameter 's' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:2995:21: style: Variable 'meta' can be declared as const array [constVariable] 2.19.0 htslib-1.22.1/vcf.c:3007:15: style: Variable 'r_start' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:3036:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:309:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:3106:13: style: Local variable 'j' shadows outer variable [shadowVariable] htslib-1.22.1/vcf.c:3062:9: note: Shadowed declaration htslib-1.22.1/vcf.c:3106:13: note: Shadow variable 2.19.0 htslib-1.22.1/vcf.c:3119:24: style: Variable 'jfmt' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:3135:46: style: Parameter 's' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:3294:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 htslib-1.22.1/vcf.c:3366:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 htslib-1.22.1/vcf.c:3399:43: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 htslib-1.22.1/vcf.c:342:38: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:3458:16: style: Condition 'ret' is always true [knownConditionTrueFalse] 2.19.0 htslib-1.22.1/vcf.c:3517:22: style: Variable 'res' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/vcf.c:3541:19: style: Variable 'max_n_flt' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/vcf.c:3722:32: portability: Casting between signed int * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 htslib-1.22.1/vcf.c:3750:23: style: Variable 't' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:380:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:396:34: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:4015:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:403:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:4072:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:4160:27: style: Variable 'id' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:418:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:4207:29: style: Variable 'missing' can be declared as const array [constVariable] 2.19.0 htslib-1.22.1/vcf.c:4234:13: style: Local variable 'i' shadows outer variable [shadowVariable] htslib-1.22.1/vcf.c:4066:9: note: Shadowed declaration htslib-1.22.1/vcf.c:4234:13: note: Shadow variable 2.19.0 htslib-1.22.1/vcf.c:4268:31: style: Variable 'id' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4347:56: style: Parameter 'v' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:4381:37: style:inconclusive: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:1204:41: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. htslib-1.22.1/vcf.c:4381:37: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. 2.19.0 htslib-1.22.1/vcf.c:4381:44: style:inconclusive: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:1204:50: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. htslib-1.22.1/vcf.c:4381:44: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. 2.19.0 htslib-1.22.1/vcf.c:4404:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:444:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:4517:49: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:4544:35: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] 2.19.0 htslib-1.22.1/vcf.c:4620:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4633:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4642:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4643:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4724:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4737:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4746:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4747:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:4769:73: style:inconclusive: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. [funcArgNamesDifferent] htslib-1.22.1/htslib/vcf.h:791:77: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. htslib-1.22.1/vcf.c:4769:73: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. 2.19.0 htslib-1.22.1/vcf.c:4787:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:493:35: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:4949:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5028:16: style: Local variable 'samples' shadows outer argument [shadowArgument] htslib-1.22.1/vcf.c:4969:53: note: Shadowed declaration htslib-1.22.1/vcf.c:5028:16: note: Shadow variable 2.19.0 htslib-1.22.1/vcf.c:5057:17: style: Local variable 'k' shadows outer variable [shadowVariable] htslib-1.22.1/vcf.c:5030:13: note: Shadowed declaration htslib-1.22.1/vcf.c:5057:17: note: Shadow variable 2.19.0 htslib-1.22.1/vcf.c:5077:59: style: Parameter 'imap' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:5088:24: style: Variable 'f' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:5227:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5238:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5302:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5464:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5579:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5600:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5618:62: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer] 2.19.0 htslib-1.22.1/vcf.c:5622:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5639:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5783:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5790:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:579:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:5820:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:589:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:5904:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:5931:18: style: Variable 'src' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:5943:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:600:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:6141:33: style: Condition 'ploidy<=1' is always true [knownConditionTrueFalse] htslib-1.22.1/vcf.c:6139:26: note: Assuming that condition 'ploidy>1' is not redundant htslib-1.22.1/vcf.c:6141:33: note: Condition 'ploidy<=1' is always true 2.19.0 htslib-1.22.1/vcf.c:6171:10: style: Variable 'e' can be declared as pointer to const [constVariablePointer] 2.19.0 htslib-1.22.1/vcf.c:6344:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable] 2.19.0 htslib-1.22.1/vcf.c:668:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition] 2.19.0 htslib-1.22.1/vcf.c:677:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition] 2.19.0 htslib-1.22.1/vcf.c:683:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition] 2.19.0 htslib-1.22.1/vcf.c:777:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 htslib-1.22.1/vcf.c:834:17: style: Local variable 'k' shadows outer variable [shadowVariable] htslib-1.22.1/vcf.c:809:13: note: Shadowed declaration htslib-1.22.1/vcf.c:834:17: note: Shadow variable DONE