2024-04-17 07:34
ftp://ftp.de.debian.org/debian/pool/main/h/htslib/htslib_1.19+ds.orig.tar.bz2
cppcheck-options: --library=posix --library=gnu --library=bsd --library=openssl --library=zlib --library=libcurl  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j4
platform: Linux-6.1.0-18-amd64-x86_64-with-glibc2.36
python: 3.11.2
client-version: 1.3.56
compiler: g++ (Debian 12.2.0-14) 12.2.0
cppcheck: head 2.13.0
head-info: 8b518bf (2024-04-17 07:27:46 +0200)
count: 1430 908
elapsed-time: 42.7 53.4
head-timing-info:

old-timing-info:

head results:
htslib-1.19/htslib/kstring.h:159:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:238:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:247:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:263:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:272:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:313:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:369:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/kstring.h:385:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/hfile.h:285:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bufsiz [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzip.c:52:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzip.c:60:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzip.c:67:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzip.c:102:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzip.c:165:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/annot-tsv.c:120:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/annot-tsv.c:305:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/annot-tsv.c:873:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/vcf.h:1213:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/vcf.h:1316:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bcf_sr_sort.c:219:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/bcf_sr_sort.c:240:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/bcf_sr_sort.c:306:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/bcf_sr_sort.c:325:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/bcf_sr_sort.c:332:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/bcf_sr_sort.c:375:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:333:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:368:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:409:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:478:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:505:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:527:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:543:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:919:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:1029:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:1543:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:1840:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:2375:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:2406:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:2473:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzf.c:2513:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/hts.h:1544:12: style: Return value '!(*((char*)(&one)))' is always false [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/htslib/hts.h:1544:12: note: Return value '!(*((char*)(&one)))' is always false
htslib-1.19/annot-tsv.c:307:19: style: Local variable 'tmp' shadows outer variable [shadowVariable]
htslib-1.19/annot-tsv.c:293:11: note: Shadowed declaration
htslib-1.19/annot-tsv.c:307:19: note: Shadow variable
htslib-1.19/annot-tsv.c:381:40: style: Parameter 'dat' can be declared as pointer to const [constParameterPointer]
htslib-1.19/annot-tsv.c:594:53: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
htslib-1.19/annot-tsv.c:685:23: style: Variable 'dst' can be declared as pointer to const [constVariablePointer]
htslib-1.19/annot-tsv.c:686:23: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
htslib-1.19/annot-tsv.c:745:17: style: Variable 'ann' can be declared as pointer to const [constVariablePointer]
htslib-1.19/annot-tsv.c:840:26: style: Variable 'loptions' can be declared as const array [constVariable]
htslib-1.19/htslib/khash_str2int.h:68:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer]
htslib-1.19/htslib/khash_str2int.h:131:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer]
htslib-1.19/htslib/kstring.h:180:39: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.19/htslib/kstring.h:196:40: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.19/bcf_sr_sort.c:323:48: style:inconclusive: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent]
htslib-1.19/bcf_sr_sort.h:103:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.19/bcf_sr_sort.c:323:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.19/bcf_sr_sort.c:330:48: style:inconclusive: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent]
htslib-1.19/bcf_sr_sort.h:104:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.19/bcf_sr_sort.c:330:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.19/bcf_sr_sort.c:583:85: style:inconclusive: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. [funcArgNamesDifferent]
htslib-1.19/bcf_sr_sort.h:102:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'.
htslib-1.19/bcf_sr_sort.c:583:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'.
htslib-1.19/bcf_sr_sort.c:42:46: style: Parameter 'bs1' can be declared as pointer to const [constParameterPointer]
htslib-1.19/bcf_sr_sort.c:42:62: style: Parameter 'bs2' can be declared as pointer to const [constParameterPointer]
htslib-1.19/bcf_sr_sort.c:223:10: style: Variable 'jmat' can be declared as pointer to const [constVariablePointer]
htslib-1.19/bcf_sr_sort.c:428:24: style: Variable 'var' can be declared as pointer to const [constVariablePointer]
htslib-1.19/bcf_sr_sort.c:540:19: style: Variable 'vset' can be declared as pointer to const [constVariablePointer]
htslib-1.19/bgzf.c:1905:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/bgzf.c:2563:27: style: Expression is always true because 'else if' condition is opposite to previous condition at line 2562. [multiCondition]
htslib-1.19/bgzf.c:2562:22: note: first condition
htslib-1.19/bgzf.c:2563:27: note: else if condition is opposite to first condition
htslib-1.19/bgzf.c:330:9: style: Condition '!ed_is_big()' is always true [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/bgzf.c:330:19: note: Calling function 'ed_is_big' returns 0
htslib-1.19/bgzf.c:330:9: note: Condition '!ed_is_big()' is always true
htslib-1.19/bgzf.c:2351:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/bgzf.c:2351:18: note: Calling function 'ed_is_big' returns 0
htslib-1.19/bgzf.c:2351:18: note: Condition 'ed_is_big()' is always false
htslib-1.19/bgzf.c:2447:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/bgzf.c:2447:18: note: Calling function 'ed_is_big' returns 0
htslib-1.19/bgzf.c:2447:18: note: Condition 'ed_is_big()' is always false
htslib-1.19/bgzf.c:1235:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero]
htslib-1.19/bgzf.c:533:25: style:inconclusive: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.19/htslib/bgzf.h:124:36: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/bgzf.c:533:25: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/bgzf.c:610:25: style:inconclusive: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. [funcArgNamesDifferent]
htslib-1.19/htslib/bgzf.h:353:29: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'.
htslib-1.19/bgzf.c:610:25: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'.
htslib-1.19/bgzf.c:2114:40: style:inconclusive: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. [funcArgNamesDifferent]
htslib-1.19/htslib/bgzf.h:283:44: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'.
htslib-1.19/bgzf.c:2114:40: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'.
htslib-1.19/bgzf.c:2221:46: style:inconclusive: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. [funcArgNamesDifferent]
htslib-1.19/htslib/bgzf.h:236:50: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'.
htslib-1.19/bgzf.c:2221:46: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'.
htslib-1.19/bgzf.c:1165:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.19/bgzf.c:1146:13: note: Shadowed declaration
htslib-1.19/bgzf.c:1165:17: note: Shadow variable
htslib-1.19/bgzf.c:1239:18: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer]
htslib-1.19/bgzf.c:2589:24: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/bgzf.c:2595:39: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/htslib/hfile.h:134:33: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/htslib/hfile.h:155:34: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/textutils_internal.h:345:19: style: Variable 'D' can be declared as const array [constVariable]
htslib-1.19/htslib/sam.h:1628:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/htslib/sam.h:1699:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:753:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:801:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:965:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:995:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:1456:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:1641:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:1734:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:1810:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:2187:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:2781:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:2820:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/bgzip.c:413:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.19/bgzip.c:137:51: note: Shadowed declaration
htslib-1.19/bgzip.c:413:17: note: Shadow variable
htslib-1.19/bgzip.c:454:49: style: Variable 'ext' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:175:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_decode.c:2340:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_decode.c:2972:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam_internal.h:56:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_encode.c:1258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_encode.c:3257:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_encode.c:4140:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_external.c:609:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RANS_ORDER_X32 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_codecs.c:2952:62: style: Condition 'option==E_BYTE' is always false [knownConditionTrueFalse]
htslib-1.19/cram/cram_codecs.c:2983:17: style: Condition 'sym>=-1' is always true [knownConditionTrueFalse]
htslib-1.19/cram/cram_codecs.c:2982:19: note: Assignment 'sym=*syms++', assigned value is greater than -1
htslib-1.19/cram/cram_codecs.c:2983:17: note: Condition 'sym>=-1' is always true
htslib-1.19/cram/cram_codecs.c:3108:33: warning: Either the condition '!tmp' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
htslib-1.19/cram/cram_codecs.c:3110:9: note: Assuming that condition '!tmp' is not redundant
htslib-1.19/cram/cram_codecs.c:3108:33: note: Null pointer addition
htslib-1.19/cram/cram_codecs.c:2119:5: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
htslib-1.19/cram/cram_codecs.c:3196:17: style: Local variable 'k' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_codecs.c:3165:44: note: Shadowed declaration
htslib-1.19/cram/cram_codecs.c:3196:17: note: Shadow variable
htslib-1.19/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-1.19/cram/cram_codecs.c:4019:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:390:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:393:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:4021:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:410:70: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:413:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:504:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:439:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:440:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:505:20: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:450:68: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4022:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:548:37: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4014:20: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:562:68: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:793:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:737:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:738:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:794:20: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:748:66: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:813:15: style: Variable 'i32' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:820:14: style: Variable 'i32' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:827:15: style: Variable 'i64' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:834:14: style: Variable 'i64' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:4031:20: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:845:66: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:3885:5: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:869:49: note: Parameter 'st' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:982:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:924:60: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:984:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:934:59: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:986:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:945:60: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:960:40: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:960:59: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1003:35: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1003:54: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1004:29: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4008:20: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1008:65: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:3887:5: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1031:48: note: Parameter 'st' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4090:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1055:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4088:26: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1073:92: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4092:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1091:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4087:20: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1167:34: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:1192:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:1204:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:1216:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:4103:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1327:94: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4105:30: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1342:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4107:30: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1391:94: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4102:19: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1521:35: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:1566:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:1577:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:4108:24: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1587:34: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1667:41: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1667:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1667:75: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1667:85: note: Parameter 'out' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1667:95: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1780:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1671:94: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:1688:55: style: Parameter 'slice' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_codecs.c:1688:74: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1692:41: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1692:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1692:75: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1692:85: note: Parameter 'out' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1692:95: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:1785:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1703:47: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:1873:19: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:1886:18: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:2023:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1914:35: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1949:41: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1949:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1950:34: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1954:40: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1954:59: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:1955:33: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:1977:19: style: Variable 'in16' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2046:39: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2046:58: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2046:73: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2046:83: note: Parameter 'out' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2046:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2051:38: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2051:57: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2051:72: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2051:82: note: Parameter 'out' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2051:92: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2185:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2108:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2409:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2286:35: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2341:39: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2341:58: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2342:34: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2347:38: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2347:57: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2348:33: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2507:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2434:90: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2582:17: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2528:89: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2623:42: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2623:61: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2624:42: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2624:52: note: Parameter 'out' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2624:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4063:26: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2629:63: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4065:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2643:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4067:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2678:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4069:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2691:61: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4071:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2728:63: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4073:31: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2741:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2971:43: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2971:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:2972:37: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:2979:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3007:42: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3007:61: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3008:36: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:3015:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3044:43: note: Parameter 'slice' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3044:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3045:37: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:3052:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/cram/cram_codecs.c:4053:20: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3094:67: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:4124:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3484:44: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/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-1.19/cram/cram_codecs.c:3673:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3563:76: note: Parameter 'c' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:3604:25: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:3623:24: style: Variable 'cp_start' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_codecs.c:3704:39: 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-1.19/cram/cram_codecs.c:4145:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3704:39: note: Parameter 'in' can be declared as pointer to const
htslib-1.19/cram/cram_codecs.c:3720:45: 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-1.19/cram/cram_codecs.c:4144:21: note: You might need to cast the function pointer here
htslib-1.19/cram/cram_codecs.c:3720:45: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.19/cram/cram_io.h:640:49: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_codecs.h:230:52: style: Parameter 'blk' can be declared as pointer to const [constParameterPointer]
htslib-1.19/htslib/sam.h:966:50: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_codecs.c:1661:60: error: Shifting signed 32-bit value by 31 bits is undefined behaviour [shiftTooManyBitsSigned]
htslib-1.19/cram/cram_structs.h:67:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.19/cram/cram_external.c:779:8: style: Redundant initialization for 'op'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.19/cram/cram_external.c:770:14: note: op is initialized
htslib-1.19/cram/cram_external.c:779:8: note: op is overwritten
htslib-1.19/cram/cram_external.c:609:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:610:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:611:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:612:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:613:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:614:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:622:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:623:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:624:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:625:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:626:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/cram/cram_external.c:58:40: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:61:34: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:64:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:65:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:67:32: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:75:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:84:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:92:56: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:96:54: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:104:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:120:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:490:61: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:494:59: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:498:54: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:515:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:516:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:517:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:518:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:519:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:520:58: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:523:64: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:544:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:558:50: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_external.c:739:49: style: Parameter 'out_rg' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_index.c:666:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_index.c:704:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_index.c:741:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_index.c:832:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId32 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:1512:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:1805:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fqz_slice [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:2475:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:2508:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:2685:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:2846:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:2964:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:3877:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:4310:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:4857:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:4971:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:5703:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:5996:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_encode.c:828:11: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.19/cram/cram_encode.c:818:11: note: First condition
htslib-1.19/cram/cram_encode.c:828:11: note: Second condition
htslib-1.19/cram/cram_encode.c:3225:27: 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-1.19/cram/cram_encode.c:3226:28: note: Assignment 'c->ref_seq_id=s->hdr->ref_seq_id'
htslib-1.19/cram/cram_encode.c:3225:27: note: Condition 'c->ref_seq_id!=s->hdr->ref_seq_id' is redundant
htslib-1.19/cram/cram_encode.c:4091:25: style: Condition 'c->refs_used' is always true [knownConditionTrueFalse]
htslib-1.19/cram/cram_encode.c:851:13: style: Variable 'methodF' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.19/cram/cram_encode.c:843:17: note: methodF is assigned
htslib-1.19/cram/cram_encode.c:851:13: note: methodF is overwritten
htslib-1.19/cram/cram_encode.c:1681:25: style: The comparison 'ret < 0' is always false. [knownConditionTrueFalse]
htslib-1.19/cram/cram_encode.c:1646:15: note: 'ret' is assigned value '0' here.
htslib-1.19/cram/cram_encode.c:1681:25: note: The comparison 'ret < 0' is always false.
htslib-1.19/cram/cram_encode.c:125:13: style: Local variable 'r' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:88:16: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:125:13: note: Shadow variable
htslib-1.19/cram/cram_encode.c:659:22: style: Local variable 'i32' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:579:13: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:659:22: note: Shadow variable
htslib-1.19/cram/cram_encode.c:955:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:804:28: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:955:13: note: Shadow variable
htslib-1.19/cram/cram_encode.c:973:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:804:28: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:973:13: note: Shadow variable
htslib-1.19/cram/cram_encode.c:1649:13: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:1646:9: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:1649:13: note: Shadow variable
htslib-1.19/cram/cram_encode.c:2850:13: style: Local variable 'key' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:2765:11: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:2850:13: note: Shadow variable
htslib-1.19/cram/cram_encode.c:2887:25: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.19/cram/cram_encode.c:2754:55: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:2887:25: note: Shadow variable
htslib-1.19/cram/cram_encode.c:3691:24: style: Local variable 'brg' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:3681:20: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:3691:24: note: Shadow variable
htslib-1.19/cram/cram_encode.c:3722:25: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_encode.c:3336:9: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:3722:25: note: Shadow variable
htslib-1.19/cram/cram_encode.c:3724:39: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.19/cram/cram_encode.c:3332:58: note: Shadowed declaration
htslib-1.19/cram/cram_encode.c:3724:39: note: Shadow variable
htslib-1.19/cram/cram_encode.c:573:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:803:61: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:1246:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:1304:14: style: Variable 'TC' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:1340:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:1401:20: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:1433:36: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:1477:29: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:1477:58: style: Parameter 'skip' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:1550:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:1657:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:1661:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:1674:28: style: Variable 'L16' can be declared as const array [constVariable]
htslib-1.19/cram/cram_encode.c:1790:21: style: Variable 'm5tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:1795:11: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:1873:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:2544:59: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:2599:51: style: Parameter 'base' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:2653:54: style: Parameter 'base' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_encode.c:3457:27: style: Variable 'sp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:3458:27: style: Variable 'rp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:3459:27: style: Variable 'qp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:3681:20: style: Variable 'brg' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:3691:24: style: Variable 'brg' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:3715:19: style: Variable 'from' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_encode.c:3750:19: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam_internal.h:71:41: style: Parameter 'nib' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_stats.c:95:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_index.c:474:30: style: Condition 'from->e[k].start<pos' is always true [knownConditionTrueFalse]
htslib-1.19/cram/cram_index.c:469:30: note: Assuming that condition 'from->e[k].start>=pos' is not redundant
htslib-1.19/cram/cram_index.c:474:30: note: Condition 'from->e[k].start<pos' is always true
htslib-1.19/cram/cram_index.c:405:42: style:inconclusive: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. [funcArgNamesDifferent]
htslib-1.19/cram/cram_index.h:54:81: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'.
htslib-1.19/cram/cram_index.c:405:42: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'.
htslib-1.19/cram/cram_index.c:568:50: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_index.c:570:17: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_index.c:569:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
htslib-1.19/cram/mFILE.c:157:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/mFILE.c:182:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/mFILE.c:198:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/mFILE.c:463:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/mFILE.c:520:13: style: Condition 'len!=size*nmemb' is always true [knownConditionTrueFalse]
htslib-1.19/cram/mFILE.c:511:9: note: len is assigned 'size*nmemb<=mf->size-mf->offset?size*nmemb:mf->size-mf->offset' here.
htslib-1.19/cram/mFILE.c:514:9: note: Assuming condition is false
htslib-1.19/cram/mFILE.c:520:13: note: Condition 'len!=size*nmemb' is always true
htslib-1.19/cram/mFILE.c:264:47: style:inconclusive: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. [funcArgNamesDifferent]
htslib-1.19/cram/mFILE.h:64:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'.
htslib-1.19/cram/mFILE.c:264:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'.
htslib-1.19/cram/mFILE.c:471:20: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/mFILE.c:494:18: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/mFILE.c:527:22: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/open_trace_file.c:195:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_decode.c:2306:19: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.19/cram/cram_decode.c:2305:19: note: First condition
htslib-1.19/cram/cram_decode.c:2306:19: note: Second condition
htslib-1.19/cram/open_trace_file.c:131:31: style: Condition 'i>0' is always true [knownConditionTrueFalse]
htslib-1.19/cram/open_trace_file.c:131:20: note: Assuming that condition 'i==0' is not redundant
htslib-1.19/cram/open_trace_file.c:131:31: note: Condition 'i>0' is always true
htslib-1.19/cram/open_trace_file.c:203:38: style: Checking if unsigned expression 'mfwrite(buf,len,1,mf)' is less than zero. [unsignedLessThanZero]
htslib-1.19/cram/open_trace_file.c:229:50: style: Parameter 'dirname' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/open_trace_file.c:232:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/open_trace_file.c:330:48: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/open_trace_file.c:330:60: style: Parameter 'relative_to' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_decode.c:1512:29: style: Variable 'md_dist' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.19/cram/cram_decode.c:1499:37: note: md_dist is assigned
htslib-1.19/cram/cram_decode.c:1512:29: note: md_dist is overwritten
htslib-1.19/cram/string_alloc.c:121:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero]
htslib-1.19/cram/cram_decode.c:2275:34: style:inconclusive: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. [funcArgNamesDifferent]
htslib-1.19/cram/cram_decode.h:105:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'.
htslib-1.19/cram/cram_decode.c:2275:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'.
htslib-1.19/cram/cram_decode.c:881:21: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.19/cram/cram_decode.c:875:72: note: Shadowed declaration
htslib-1.19/cram/cram_decode.c:881:21: note: Shadow variable
htslib-1.19/cram/cram_decode.c:1505:38: style: Local variable 'r' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_decode.c:1099:26: note: Shadowed declaration
htslib-1.19/cram/cram_decode.c:1505:38: note: Shadow variable
htslib-1.19/cram/cram_decode.c:1916:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_decode.c:1903:19: note: Shadowed declaration
htslib-1.19/cram/cram_decode.c:1916:21: note: Shadow variable
htslib-1.19/cram/cram_decode.c:1985:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_decode.c:1957:19: note: Shadowed declaration
htslib-1.19/cram/cram_decode.c:1985:21: note: Shadow variable
htslib-1.19/cram/cram_decode.c:2869:31: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.19/cram/cram_decode.c:2274:52: note: Shadowed declaration
htslib-1.19/cram/cram_decode.c:2869:31: note: Shadow variable
htslib-1.19/cram/cram_decode.c:552:41: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_decode.c:875:55: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_decode.c:926:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:938:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:1229:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:1708:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:1713:35: style: Variable 'refp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:1814:28: style: Variable 'orig_aux_p' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:1888:58: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_decode.c:2233:39: style: Parameter 'md5' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_decode.c:2250:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_decode.c:2286:18: style: Variable 'bfd' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:2435:25: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:3007:48: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_decode.c:3013:11: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_decode.c:3013:17: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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]
htslib-1.19/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]
htslib-1.19/cram/cram_decode.c:1419:34: style: Variable 'dlen' is assigned a value that is never used. [unreadVariable]
htslib-1.19/errmod.c:93:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
htslib-1.19/faidx.c:83:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.19/faidx.c:341:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.19/faidx.c:384:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SCNu64 [valueFlowBailoutIncompleteVar]
htslib-1.19/faidx.c:496:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/faidx.c:586:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/faidx.c:699:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/errmod.c:34:1: style: Parameter 'array' can be declared as const array [constParameter]
htslib-1.19/cram/cram_stats.c:168:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/cram/cram_stats.c:135:16: note: Shadowed declaration
htslib-1.19/cram/cram_stats.c:168:13: note: Shadow variable
htslib-1.19/header.c:189:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:735:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:767:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SSIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:1070:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:1101:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:1209:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:1936:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:1967:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/faidx.c:218:31: style: Condition 'c!='\n'' is always true [knownConditionTrueFalse]
htslib-1.19/faidx.c:216:27: note: Assuming that condition 'c=='+'' is not redundant
htslib-1.19/faidx.c:218:31: note: Condition 'c!='\n'' is always true
htslib-1.19/faidx.c:705:24: style: Checking if unsigned expression 'val->line_blen' is less than zero. [unsignedLessThanZero]
htslib-1.19/faidx.c:780:59: style:inconclusive: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.19/htslib/faidx.h:201:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:780:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:792:51: style:inconclusive: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.19/htslib/faidx.h:192:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:792:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:805:49: style:inconclusive: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.19/htslib/faidx.h:190:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:805:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:813:55: style:inconclusive: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.19/htslib/faidx.h:217:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:813:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:825:53: style:inconclusive: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.19/htslib/faidx.h:215:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:825:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.19/faidx.c:865:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_gcs.c:75:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_gcs.c:145:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gcs_vopen [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:157:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:187:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:230:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:240:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:286:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:320:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:360:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:371:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:382:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:406:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:422:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:443:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:488:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:501:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:543:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:554:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:599:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:618:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:654:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:725:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:753:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:786:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:824:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:870:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:891:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hopenv_mem [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:919:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:1033:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:1135:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_gcs.c:104:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/hfile_gcs.c:105:24: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/hfile_gcs.c:112:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/hfile_libcurl.c:131:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOSYS [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:160:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:240:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EBADF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:282:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:315:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:329:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:370:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:513:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:568:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:701:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLM_OK [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:750:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_WRITEFUNC_PAUSE [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:767:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:826:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:870:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_READFUNC_PAUSE [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:889:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:934:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:1016:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:1134:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:1188:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:1436:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_libcurl.c:1505:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vhopen_libcurl [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile.c:1026:57: style: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true [knownConditionTrueFalse]
htslib-1.19/hfile.c:1026:39: note: Calling function 'try_exe_add_scheme_handler' returns -1
htslib-1.19/hfile.c:1026:57: note: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true
htslib-1.19/hfile.c:1281:26: style:inconclusive: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent]
htslib-1.19/htslib/hfile.h:74:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.19/hfile.c:1281:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.19/hfile.c:1309:27: style:inconclusive: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent]
htslib-1.19/htslib/hfile.h:99:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.19/hfile.c:1309:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.19/hfile.c:1329:46: style:inconclusive: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. [funcArgNamesDifferent]
htslib-1.19/htslib/hfile.h:114:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'.
htslib-1.19/hfile.c:1329:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'.
htslib-1.19/hfile.c:163:50: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile.c:235:11: style: Variable 'found' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile.c:572:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile.c:586:28: 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-1.19/hfile.c:624:33: note: You might need to cast the function pointer here
htslib-1.19/hfile.c:586:28: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.19/hfile.c:606:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile.c:784:30: 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-1.19/hfile.c:797:17: note: You might need to cast the function pointer here
htslib-1.19/hfile.c:784:30: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.19/hfile.c:790:29: style: Parameter 'fpv' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile.c:868:35: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile.c:1367:9: style: struct member 'knetFile_s::type' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1369:11: style: struct member 'knetFile_s::host' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1369:18: style: struct member 'knetFile_s::port' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1370:9: style: struct member 'knetFile_s::ctrl_fd' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1370:18: style: struct member 'knetFile_s::pasv_ip' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1370:30: style: struct member 'knetFile_s::pasv_port' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1370:41: style: struct member 'knetFile_s::max_response' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1370:55: style: struct member 'knetFile_s::no_reconnect' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1370:69: style: struct member 'knetFile_s::is_ready' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1371:11: style: struct member 'knetFile_s::response' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1371:22: style: struct member 'knetFile_s::retr' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1371:29: style: struct member 'knetFile_s::size_cmd' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1372:13: style: struct member 'knetFile_s::seek_offset' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1373:13: style: struct member 'knetFile_s::file_size' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1374:11: style: struct member 'knetFile_s::path' is never used. [unusedStructMember]
htslib-1.19/hfile.c:1374:18: style: struct member 'knetFile_s::http_host' is never used. [unusedStructMember]
htslib-1.19/hfile_s3.c:126:0: error: #error No HMAC() routine found by configure [preprocessorErrorDirective]
htslib-1.19/hfile_s3_write.c:157:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:170:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:216:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:256:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_CUSTOMREQUEST [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:322:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_POST [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:404:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_UPLOAD [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:440:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:506:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLINFO_RESPONSE_CODE [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:572:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:613:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_URL [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:649:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:682:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:779:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:804:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:826:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:839:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vhopen_s3_write [valueFlowBailoutIncompleteVar]
htslib-1.19/hfile_s3_write.c:165:38: style: Parameter 'start_tag' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_s3_write.c:165:55: style: Parameter 'end_tag' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_s3_write.c:167:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_s3_write.c:286:59: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_s3_write.c:371:55: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_s3_write.c:584:61: style: Parameter 'head' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_s3_write.c:584:78: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_s3_write.c:662:64: style: Parameter 'auth' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_s3_write.c:798:22: style: Variable 'args2' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_libcurl.c:797:23: style: Condition 'bytes<n' is always false [knownConditionTrueFalse]
htslib-1.19/hfile_libcurl.c:795:26: note: bytes is assigned 'n<=nbytes?n:nbytes' here.
htslib-1.19/hfile_libcurl.c:797:23: note: Condition 'bytes<n' is always false
htslib-1.19/hfile_libcurl.c:418:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_libcurl.c:561:15: style: Variable 'header' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_libcurl.c:743:35: style: Parameter 'ptr' can be declared as pointer to const. However it seems that 'recv_callback' is a callback function, if 'ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
htslib-1.19/hfile_libcurl.c:1228:66: note: You might need to cast the function pointer here
htslib-1.19/hfile_libcurl.c:743:35: note: Parameter 'ptr' can be declared as pointer to const
htslib-1.19/hfile_libcurl.c:794:19: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_libcurl.c:1014:28: style: Variable 'list' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_libcurl.c:1168:64: style: Parameter 'headers' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hfile_libcurl.c:1171:24: style: Variable 'list' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_libcurl.c:1245:15: style: Variable 'env_curl_ca_bundle' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hfile_libcurl.c:1414:22: style: Variable 'args2' can be declared as pointer to const [constVariablePointer]
htslib-1.19/htslib/hts_expr.h:80:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
htslib-1.19/hts_expr.c:268:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/hts_expr.c:292:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/hts_expr.c:751:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REG_EXTENDED [valueFlowBailoutIncompleteVar]
htslib-1.19/hts_expr.c:879:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/header.c:191:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/header.c:672:43: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/header.c:1104:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/header.c:1335:47: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/header.c:2313:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/header.c:2329:65: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/header.c:1207:34: style:inconclusive: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:445:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1207:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1214:36: style:inconclusive: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:458:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1214:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1221:35: style:inconclusive: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:465:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1221:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1286:34: style:inconclusive: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:483:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1286:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1321:33: style:inconclusive: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:499:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1321:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1354:37: style:inconclusive: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:518:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1354:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1378:38: style:inconclusive: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:536:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1378:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1412:39: style:inconclusive: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:561:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1412:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1451:40: style:inconclusive: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:573:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1451:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1538:36: style:inconclusive: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:600:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1538:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1643:38: style:inconclusive: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:617:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1643:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1699:37: style:inconclusive: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:657:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1699:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1699:81: style:inconclusive: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:657:80: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'.
htslib-1.19/header.c:1699:81: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'.
htslib-1.19/header.c:1771:36: style:inconclusive: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:666:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1771:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1911:36: style:inconclusive: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:707:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1911:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1943:37: style:inconclusive: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:725:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1943:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1974:38: style:inconclusive: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:736:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:1974:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2021:33: style:inconclusive: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:749:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2021:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2190:38: style:inconclusive: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:792:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2190:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2241:31: style:inconclusive: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:810:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2241:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2346:34: style:inconclusive: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:830:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:2346:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/header.c:66:64: style: Parameter 'type_list' can be declared as pointer to const [constParameterPointer]
htslib-1.19/header.c:587:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:587:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:624:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:624:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:733:10: style: Variable 'c' can be declared as const array [constVariable]
htslib-1.19/header.c:1177:22: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1366:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1390:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1500:11: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1502:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1701:15: style: Variable 'rh' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1729:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1745:22: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1931:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:1962:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:2498:27: style: Variable 't2' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:2573:15: style: Variable 'k' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:2573:19: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:2671:25: style: Variable 'sn_tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/header.c:41:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.19/header.c:1750:17: style: Variable 'head' is assigned a value that is never used. [unreadVariable]
htslib-1.19/htsfile.c:51:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/htsfile.c:72:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/htsfile.c:116:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/htsfile.c:155:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/htsfile.c:257:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/cram/cram_io.c:4318:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/cram/cram_io.c:2398:11: warning: Either the condition '!r' is redundant or there is possible null pointer dereference: r. [nullPointerRedundantCheck]
htslib-1.19/cram/cram_io.c:2401:9: note: Assuming that condition '!r' is not redundant
htslib-1.19/cram/cram_io.c:2398:11: note: Null pointer dereference
htslib-1.19/cram/cram_io.c:5228:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.19/cram/cram_io.c:5227:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
htslib-1.19/cram/cram_io.c:5228:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
htslib-1.19/cram/cram_io.c:5229:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.19/cram/cram_io.c:5228:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
htslib-1.19/cram/cram_io.c:5229:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
htslib-1.19/cram/cram_io.c:5230:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.19/cram/cram_io.c:5229:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
htslib-1.19/cram/cram_io.c:5230:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
htslib-1.19/cram/cram_io.c:4909:61: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/cram/cram_io.c:4966:93: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/cram/cram_io.c:4973:95: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/cram/cram_io.c:137:39: style:inconclusive: Function 'itf8_decode' argument 2 names different: declaration 'val' definition 'val_p'. [funcArgNamesDifferent]
htslib-1.19/cram/cram_io.h:69:39: note: Function 'itf8_decode' argument 2 names different: declaration 'val' definition 'val_p'.
htslib-1.19/cram/cram_io.c:137:39: note: Function 'itf8_decode' argument 2 names different: declaration 'val' definition 'val_p'.
htslib-1.19/cram/cram_io.c:4025:55: style:inconclusive: Function 'cram_write_container' argument 2 names different: declaration 'h' definition 'c'. [funcArgNamesDifferent]
htslib-1.19/htslib/cram.h:553:55: note: Function 'cram_write_container' argument 2 names different: declaration 'h' definition 'c'.
htslib-1.19/cram/cram_io.c:4025:55: note: Function 'cram_write_container' argument 2 names different: declaration 'h' definition 'c'.
htslib-1.19/cram/cram_io.c:3757:29: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.19/cram/cram_io.c:3707:42: note: Shadowed declaration
htslib-1.19/cram/cram_io.c:3757:29: note: Shadow variable
htslib-1.19/cram/cram_io.c:138:16: style: Variable 'nbytes' can be declared as const array [constVariable]
htslib-1.19/cram/cram_io.c:146:16: style: Variable 'nbits' can be declared as const array [constVariable]
htslib-1.19/cram/cram_io.c:196:16: style: Variable 'nbytes' can be declared as const array [constVariable]
htslib-1.19/cram/cram_io.c:204:16: style: Variable 'nbits' can be declared as const array [constVariable]
htslib-1.19/cram/cram_io.c:1928:9: style: Variable 'methmap' can be declared as const array [constVariable]
htslib-1.19/cram/cram_io.c:2112:24: style: Variable 'meth_cost' can be declared as const array [constVariable]
htslib-1.19/cram/cram_io.c:2471:44: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_io.c:2765:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_io.c:2825:45: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_io.c:2843:48: style: Parameter 'dir' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_io.c:2844:16: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_io.c:3268:15: style: Variable 'cp_to' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_io.c:3509:28: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_io.c:3949:41: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_io.c:4854:40: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_io.c:4923:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_io.c:5279:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_io.c:5669:23: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.19/cram/cram_io.c:5809:21: style: Variable 'r' can be declared as pointer to const [constVariablePointer]
htslib-1.19/cram/cram_io.c:2279:15: style: Variable 'strat' is assigned a value that is never used. [unreadVariable]
htslib-1.19/cram/cram_io.c:3510:25: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
htslib-1.19/hts.c:86:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_VERSION_TEXT [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:152:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_CC [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:949:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:1457:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:1644:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:1937:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:1979:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2011:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2070:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2160:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2161:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2432:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2484:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2699:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2781:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2832:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:2894:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:3031:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:3265:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:3629:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4003:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4097:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4161:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4494:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4728:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4814:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4850:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4911:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:4987:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/kstring.c:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/kstring.c:277:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/kstring.c:310:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/kstring.c:187:44: style:inconclusive: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'. [funcArgNamesDifferent]
htslib-1.19/htslib/kstring.h:117:45: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
htslib-1.19/kstring.c:187:44: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
htslib-1.19/kstring.c:379:31: style: Variable 'bmBc' can be declared as pointer to const [constVariablePointer]
htslib-1.19/md5.c:271:35: style:inconclusive: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:1487:39: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'.
htslib-1.19/md5.c:271:35: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'.
htslib-1.19/multipart.c:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/multipart.c:122:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/multipart.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/multipart.c:259:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/plugin.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/plugin.c:77:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUGIN_EXT [valueFlowBailoutIncompleteVar]
htslib-1.19/plugin.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/plugin.c:190:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/plugin.c:108:21: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
htslib-1.19/plugin.c:107:24: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.19/multipart.c:89:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/multipart.c:90:68: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/multipart.c:114:39: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'multipart_write' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
htslib-1.19/multipart.c:140:21: note: You might need to cast the function pointer here
htslib-1.19/multipart.c:114:39: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.19/multipart.c:120:36: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'multipart_seek' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
htslib-1.19/multipart.c:140:38: note: You might need to cast the function pointer here
htslib-1.19/multipart.c:120:36: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.19/realn.c:94:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/realn.c:216:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/probaln.c:86:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/hts_expr.c:104:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.19/hts_expr.c:101:14: note: l is initialized
htslib-1.19/hts_expr.c:104:12: note: l is overwritten
htslib-1.19/hts_expr.c:121:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.19/hts_expr.c:118:14: note: l is initialized
htslib-1.19/hts_expr.c:121:12: note: l is overwritten
htslib-1.19/hts_expr.c:138:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.19/hts_expr.c:135:14: note: l is initialized
htslib-1.19/hts_expr.c:138:12: note: l is overwritten
htslib-1.19/hts_expr.c:48:9: style: struct member 'hts_filter_t::parsed' is never used. [unusedStructMember]
htslib-1.19/regidx.c:164:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/probaln.c:182:16: style: Variable 'E' can be declared as const array [constVariable]
htslib-1.19/probaln.c:305:16: style: Variable 'E' can be declared as const array [constVariable]
htslib-1.19/probaln.c:381:27: style: Variable 'fi' can be declared as pointer to const [constVariablePointer]
htslib-1.19/probaln.c:381:46: style: Variable 'bi' can be declared as pointer to const [constVariablePointer]
htslib-1.19/probaln.c:416:25: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
htslib-1.19/region.c:43:21: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
htslib-1.19/region.c:44:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/region.c:87:35: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/regidx.c:440:68: style: Condition 'list->reg[ireg].beg<=end' is always true [knownConditionTrueFalse]
htslib-1.19/regidx.c:439:38: note: Assuming that condition 'list->reg[ireg].beg>end' is not redundant
htslib-1.19/regidx.c:440:68: note: Condition 'list->reg[ireg].beg<=end' is always true
htslib-1.19/regidx.c:631:63: style: Condition 'list->reg[i].beg<=itr->end' is always true [knownConditionTrueFalse]
htslib-1.19/regidx.c:630:31: note: Assuming that condition 'list->reg[i].beg>itr->end' is not redundant
htslib-1.19/regidx.c:631:63: note: Condition 'list->reg[i].beg<=itr->end' is always true
htslib-1.19/regidx.c:209:42: style:inconclusive: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:150:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
htslib-1.19/regidx.c:209:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
htslib-1.19/regidx.c:209:119: style:inconclusive: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:150:121: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.19/regidx.c:209:119: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.19/regidx.c:246:114: style:inconclusive: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:148:113: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.19/regidx.c:246:114: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.19/regidx.c:401:30: style:inconclusive: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:167:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.19/regidx.c:401:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.19/regidx.c:401:95: style:inconclusive: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:167:92: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:401:95: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:584:33: style:inconclusive: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:212:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.19/regidx.c:584:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.19/regidx.c:599:29: style:inconclusive: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:216:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.19/regidx.c:599:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.19/regidx.c:599:47: style:inconclusive: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:216:44: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:599:47: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:606:31: style:inconclusive: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:214:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:606:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:612:30: style:inconclusive: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:223:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:612:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:646:27: style:inconclusive: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.19/htslib/regidx.h:230:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:646:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.19/regidx.c:105:35: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.19/regidx.c:132:35: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
htslib-1.19/regidx.c:132:45: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.19/regidx.c:151:38: style: Parameter 'chr_beg' can be declared as pointer to const [constParameterPointer]
htslib-1.19/regidx.c:151:53: style: Parameter 'chr_end' can be declared as pointer to const [constParameterPointer]
htslib-1.19/regidx.c:151:98: style: Parameter 'payload' can be declared as pointer to const [constParameterPointer]
htslib-1.19/regidx.c:684:13: style: Variable 'src_itr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/regidx.c:48:15: style: struct member 'pos_t::pos' is never used. [unusedStructMember]
htslib-1.19/regidx.c:49:15: style: struct member 'pos_t::ireg' is never used. [unusedStructMember]
htslib-1.19/realn.c:58:51: style: Condition 'qual[z]>=13' is always true [knownConditionTrueFalse]
htslib-1.19/realn.c:56:53: note: Assuming that condition 'qual[z]>=13' is not redundant
htslib-1.19/realn.c:58:51: note: Condition 'qual[z]>=13' is always true
htslib-1.19/realn.c:41:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/realn.c:42:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/realn.c:43:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
htslib-1.19/realn.c:111:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/realn.c:112:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
htslib-1.19/realn.c:205:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/realn.c:48:27: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
htslib-1.19/realn.c:73:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
htslib-1.19/realn.c:77:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
htslib-1.19/samples/add_header.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/cram.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/cram.c:53:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/dump_aux.c:126:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/dump_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/flags_demo.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/flags_demo.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/flags_htsopt_field.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/flags_htsopt_field.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/index_multireg_read.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/index_multireg_read.c:117:11: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
htslib-1.19/samples/index_reg_read.c:68:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/index_write.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/mod_aux.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/mod_aux.c:115:27: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
htslib-1.19/samples/mod_aux_ba.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/mod_aux_ba.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/mod_bam.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/modstate.c:64:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/sam_mods.c:205:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam_mods.c:247:14: style: Variable 'mi' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam_mods.c:263:14: style: Variable 'ml_end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam_mods.c:293:29: style: Variable 'me' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam_mods.c:477:15: style: Variable 'MMptr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam_mods.c:635:44: style: Parameter 'state' can be declared as pointer to const [constParameterPointer]
htslib-1.19/sam_mods.c:273:18: style: Variable 'implicit' is assigned a value that is never used. [unreadVariable]
htslib-1.19/samples/mpileup.c:96:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/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-1.19/samples/mpileup.c:138:36: note: You might need to cast the function pointer here
htslib-1.19/samples/mpileup.c:56:26: note: Parameter 'data' can be declared as pointer to const
htslib-1.19/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-1.19/samples/mpileup.c:138:36: note: You might need to cast the function pointer here
htslib-1.19/samples/mpileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const
htslib-1.19/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-1.19/samples/mpileup.c:139:35: note: You might need to cast the function pointer here
htslib-1.19/samples/mpileup.c:60:25: note: Parameter 'data' can be declared as pointer to const
htslib-1.19/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-1.19/samples/mpileup.c:139:35: note: You might need to cast the function pointer here
htslib-1.19/samples/mpileup.c:60:63: note: Parameter 'cd' can be declared as pointer to const
htslib-1.19/samples/pileup.c:104:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/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-1.19/samples/pileup.c:131:34: note: You might need to cast the function pointer here
htslib-1.19/samples/pileup.c:56:26: note: Parameter 'data' can be declared as pointer to const
htslib-1.19/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-1.19/samples/pileup.c:131:34: note: You might need to cast the function pointer here
htslib-1.19/samples/pileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const
htslib-1.19/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-1.19/samples/pileup.c:132:33: note: You might need to cast the function pointer here
htslib-1.19/samples/pileup.c:65:25: note: Parameter 'data' can be declared as pointer to const
htslib-1.19/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-1.19/samples/pileup.c:132:33: note: You might need to cast the function pointer here
htslib-1.19/samples/pileup.c:65:63: note: Parameter 'cd' can be declared as pointer to const
htslib-1.19/samples/modstate.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/modstate.c:56:77: style: Variable 'bm' can be declared as pointer to const [constVariablePointer]
htslib-1.19/samples/pileup_mod.c:109:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/read_aux.c:122:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/read_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/read_bam.c:63:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/read_fast.c:58:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/read_fast.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/read_bam.c:114:18: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/samples/read_bam.c:55:20: note: Shadowed declaration
htslib-1.19/samples/read_bam.c:114:18: note: Shadow variable
htslib-1.19/samples/read_bam.c:48:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/read_header.c:56:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/read_refname.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/read_refname.c:91:12: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
htslib-1.19/samples/read_refname.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/rem_header.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/rem_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/split.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/split.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/split2.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/split2.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/split_thread1.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/split_thread2.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/split_thread1.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/split_thread2.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/write_fast.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:436:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:554:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:683:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:832:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:913:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:980:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:1092:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:1863:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:2157:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:2188:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:2323:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:2766:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:3166:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EIO [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:3263:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:3418:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:3529:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:3693:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4057:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4094:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4204:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4303:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4328:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4539:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4652:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4696:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4705:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4732:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4739:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4749:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4766:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4818:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4887:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4922:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:4980:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:5006:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:5015:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:5022:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:5032:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:5042:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:5895:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:5994:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:6128:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/write_fast.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/samples/update_header.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/samples/update_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.19/tabix.c:59:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/tabix.c:71:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/tabix.c:110:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/tabix.c:163:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/tabix.c:413:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/tabix.c:534:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:86:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:126:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pair [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:201:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:220:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable targets_overlap [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:412:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:447:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:455:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:512:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:668:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:761:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:859:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:989:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:1433:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/synced_bcf_reader.c:249:34: style:inconclusive: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:237:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:249:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:434:32: style:inconclusive: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:204:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:434:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:814:33: style:inconclusive: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:251:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:814:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:885:35: style:inconclusive: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:281:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:885:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.19/synced_bcf_reader.c:885:54: style:inconclusive: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:281:56: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'.
htslib-1.19/synced_bcf_reader.c:885:54: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'.
htslib-1.19/synced_bcf_reader.c:1182:77: style:inconclusive: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:348:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'.
htslib-1.19/synced_bcf_reader.c:1182:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'.
htslib-1.19/synced_bcf_reader.c:1182:87: style:inconclusive: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:348:86: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'.
htslib-1.19/synced_bcf_reader.c:1182:87: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'.
htslib-1.19/synced_bcf_reader.c:1182:98: style:inconclusive: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:348:96: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'.
htslib-1.19/synced_bcf_reader.c:1182:98: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'.
htslib-1.19/synced_bcf_reader.c:1262:47: style:inconclusive: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:351:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.19/synced_bcf_reader.c:1262:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.19/synced_bcf_reader.c:1287:43: style:inconclusive: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:360:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.19/synced_bcf_reader.c:1287:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.19/synced_bcf_reader.c:1287:60: style:inconclusive: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:360:64: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'.
htslib-1.19/synced_bcf_reader.c:1287:60: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'.
htslib-1.19/synced_bcf_reader.c:1494:44: style:inconclusive: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. [funcArgNamesDifferent]
htslib-1.19/htslib/synced_bcf_reader.h:390:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'.
htslib-1.19/synced_bcf_reader.c:1494:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'.
htslib-1.19/synced_bcf_reader.c:1456:33: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/synced_bcf_reader.c:147:37: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/synced_bcf_reader.c:385:20: style: Variable 'hdr0' can be declared as pointer to const [constVariablePointer]
htslib-1.19/synced_bcf_reader.c:386:20: style: Variable 'hdr1' can be declared as pointer to const [constVariablePointer]
htslib-1.19/synced_bcf_reader.c:491:40: style: Parameter 'reader' can be declared as pointer to const [constParameterPointer]
htslib-1.19/synced_bcf_reader.c:491:56: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
htslib-1.19/synced_bcf_reader.c:584:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.19/synced_bcf_reader.c:585:19: style: Variable 'alt' can be declared as pointer to const [constVariablePointer]
htslib-1.19/synced_bcf_reader.c:999:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
htslib-1.19/synced_bcf_reader.c:1000:16: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.19/synced_bcf_reader.c:1332:20: style: Variable 'creg' can be declared as pointer to const [constVariablePointer]
htslib-1.19/tabix.c:199:52: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer]
htslib-1.19/tabix.c:375:81: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer]
htslib-1.19/tabix.c:382:15: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer]
htslib-1.19/tabix.c:496:11: style: Variable 'reheader' can be declared as pointer to const [constVariablePointer]
htslib-1.19/tabix.c:656:11: style: Variable 'suffix' can be declared as pointer to const [constVariablePointer]
htslib-1.19/tbx.c:162:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/tbx.c:439:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/fieldarith.c:42:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/fieldarith.c:37:14: style: Variable 'aux' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/fuzz/hts_open_fuzzer.c:46:62: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/fuzz/hts_open_fuzzer.c:121:62: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/hfile.c:40:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hfile.c:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hfile.c:107:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hts_endian.c:169:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hts_endian.c:252:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hts_endian.c:333:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hts_endian.c:415:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hts_endian.c:460:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hts_endian.c:508:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/hts_endian.c:149:31: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer]
htslib-1.19/tbx.c:248:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/tbx.c:248:18: note: Calling function 'ed_is_big' returns 0
htslib-1.19/tbx.c:248:18: note: Condition 'ed_is_big()' is always false
htslib-1.19/tbx.c:253:13: style: Local variable 'x' shadows outer variable [shadowVariable]
htslib-1.19/tbx.c:231:14: note: Shadowed declaration
htslib-1.19/tbx.c:253:13: note: Shadow variable
htslib-1.19/tbx.c:410:11: style: Variable 'nm' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup.c:135:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/pileup.c:180:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/pileup.c:216:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/pileup.c:81:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup_mod.c:155:13: style: Local variable 'n' shadows outer argument [shadowArgument]
htslib-1.19/test/pileup_mod.c:139:47: note: Shadowed declaration
htslib-1.19/test/pileup_mod.c:155:13: note: Shadow variable
htslib-1.19/test/pileup_mod.c:49:32: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/pileup_mod.c:60:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup_mod.c:61:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup_mod.c:89:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/pileup_mod.c:100:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup_mod.c:101:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup_mod.c:138:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/pileup_mod.c:149:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup_mod.c:150:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/pileup_mod.c:159:16: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
htslib-1.19/test/test-bcf-sr.c:47:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-bcf-sr.c:54:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-bcf-sr.c:145:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:64:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:112:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:156:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:213:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:318:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:901:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:992:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:1064:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:1170:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:1228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:1397:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:1516:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:1581:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:1783:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2005:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2041:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2086:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2115:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2137:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2154:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2174:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2203:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2243:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:2315:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-bcf-sr.c:75:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test-bcf-sr.c:92:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test-bcf-sr.c:125:26: style: Variable 'loptions' can be declared as const array [constVariable]
htslib-1.19/test/test-bcf-translate.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-bcf-translate.c:114:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:242:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:313:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:336:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:351:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:377:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:710:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1166:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1216:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1511:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1532:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1731:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1760:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1910:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2197:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2267:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2384:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2467:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2822:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2848:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2956:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:2992:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:3066:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:3295:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:3431:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:3490:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:3884:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:3941:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:4260:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:4620:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:4794:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5071:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5082:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5145:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5304:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5411:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5432:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5454:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5470:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5626:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5633:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5663:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5747:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:5786:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-bcf_set_variant_type.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/sam.c:443:15: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.19/test/sam.c:442:15: note: First condition
htslib-1.19/test/sam.c:443:15: note: Second condition
htslib-1.19/test/sam.c:444:15: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.19/test/sam.c:443:15: note: First condition
htslib-1.19/test/sam.c:444:15: note: Second condition
htslib-1.19/test/sam.c:445:15: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.19/test/sam.c:444:15: note: First condition
htslib-1.19/test/sam.c:445:15: note: Second condition
htslib-1.19/test/sam.c:996:27: warning: Either the condition '!text' is redundant or there is possible null pointer dereference: text. [nullPointerRedundantCheck]
htslib-1.19/test/sam.c:990:9: note: Assuming that condition '!text' is not redundant
htslib-1.19/test/sam.c:996:27: note: Null pointer dereference
htslib-1.19/test/sam.c:1068:34: warning: Either the condition '!text' is redundant or there is possible null pointer dereference: text. [nullPointerRedundantCheck]
htslib-1.19/test/sam.c:1062:13: note: Assuming that condition '!text' is not redundant
htslib-1.19/test/sam.c:1068:34: note: Null pointer dereference
htslib-1.19/test/sam.c:1664:24: style: The comparison 'no_compression != 0' is always false. [knownConditionTrueFalse]
htslib-1.19/test/sam.c:1665:14: style: The comparison 'gzip != 1' is always false. [knownConditionTrueFalse]
htslib-1.19/test/sam.c:1666:14: style: The comparison 'bgzf != 2' is always false. [knownConditionTrueFalse]
htslib-1.19/test/sam.c:763:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:766:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:770:49: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:773:55: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:781:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:784:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:787:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:851:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:956:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:960:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:964:63: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:967:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:970:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:980:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:983:61: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1055:46: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1126:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1128:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1130:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1132:73: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1139:71: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1142:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1145:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1273:64: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1276:81: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1281:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1289:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1297:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1322:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1331:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:1340:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:2248:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/test/sam.c:99:39: style: Parameter 'aln' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/sam.c:101:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/sam.c:2310:11: style: Variable 'cig' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/sam.c:48:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.19/test/sam.c:498:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
htslib-1.19/test/test-parse-reg.c:63:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-parse-reg.c:98:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-parse-reg.c:172:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-parse-reg.c:51:24: style: Parameter 'reg_exp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test-parse-reg.c:72:20: style: Parameter 'fn' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test-regidx.c:50:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:60:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:69:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:128:103: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:162:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:193:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:218:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu32 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:281:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:363:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:417:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:441:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-regidx.c:250:11: style: Variable 'beg' can be declared as pointer to const [constVariablePointer]
htslib-1.19/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-1.19/test/test-regidx.c:457:10: note: You might need to cast the function pointer here
htslib-1.19/test/test-regidx.c:307:53: note: Parameter 'chr' can be declared as pointer to const
htslib-1.19/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-1.19/test/test-regidx.c:451:10: note: You might need to cast the function pointer here
htslib-1.19/test/test-regidx.c:311:53: note: Parameter 'chr' can be declared as pointer to const
htslib-1.19/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-1.19/test/test-regidx.c:454:10: note: You might need to cast the function pointer here
htslib-1.19/test/test-regidx.c:315:53: note: Parameter 'chr' can be declared as pointer to const
htslib-1.19/test/test-regidx.c:428:26: style: Variable 'loptions' can be declared as const array [constVariable]
htslib-1.19/test/test-vcf-api.c:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:52:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:112:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:288:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:407:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:435:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:493:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:547:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test-vcf-api.c:586:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/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-1.19/test/test-vcf-api.c:69:44: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test-vcf-api.c:357:17: style: Variable 'tmpia' can be declared as const array [constVariable]
htslib-1.19/test/test-vcf-sweep.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:71:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:81:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:93:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:113:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:125:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:168:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:184:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:194:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:207:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:218:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:238:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:248:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:270:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:281:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:291:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:302:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:318:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:332:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:367:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:408:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:444:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:524:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:590:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:623:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:646:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:741:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:842:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:888:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:949:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_bgzf.c:1035:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/sam.c:3141:21: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/sam.c:3161:21: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/sam.c:3442:33: 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]
htslib-1.19/sam.c:257:17: style: Condition 'bufsize<h->l_text' is always false [knownConditionTrueFalse]
htslib-1.19/sam.c:256:13: note: bufsize is assigned 'h->l_text+1' here.
htslib-1.19/sam.c:257:17: note: Condition 'bufsize<h->l_text' is always false
htslib-1.19/sam.c:931:17: style: Condition 'new_len<1' is always false [knownConditionTrueFalse]
htslib-1.19/sam.c:930:36: note: Assignment 'new_len=strlen(qname)+1', assigned value is greater than 0
htslib-1.19/sam.c:931:17: note: Condition 'new_len<1' is always false
htslib-1.19/sam.c:5142:50: style: Condition 'strncmp(format,"fa",format_len)==0' is always false [knownConditionTrueFalse]
htslib-1.19/sam.c:5861:39: style: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true [knownConditionTrueFalse]
htslib-1.19/sam.c:5861:39: note: Calling function 'resolve_cigar2' returns 1
htslib-1.19/sam.c:5861:39: note: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true
htslib-1.19/sam.c:4328:15: warning: Either the condition 'x' is redundant or there is possible null pointer dereference: x. [nullPointerRedundantCheck]
htslib-1.19/sam.c:4332:9: note: Assuming that condition 'x' is not redundant
htslib-1.19/sam.c:4328:15: note: Null pointer dereference
htslib-1.19/sam.c:5682:29: style: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value. [duplicateExpression]
htslib-1.19/sam.c:5680:31: note: 'iref' is assigned value 'b->core.pos' here.
htslib-1.19/sam.c:5682:29: note: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value.
htslib-1.19/sam.c:2374:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/sam.c:116:33: style:inconclusive: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:385:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/sam.c:116:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.19/sam.c:924:27: style:inconclusive: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. [funcArgNamesDifferent]
htslib-1.19/htslib/sam.h:1115:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'.
htslib-1.19/sam.c:924:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'.
htslib-1.19/sam.c:2061:25: style: Local variable 'absent' shadows outer variable [shadowVariable]
htslib-1.19/sam.c:2026:20: note: Shadowed declaration
htslib-1.19/sam.c:2061:25: note: Shadow variable
htslib-1.19/sam.c:2651:19: style: Local variable 'end' shadows outer argument [shadowArgument]
htslib-1.19/sam.c:2545:48: note: Shadowed declaration
htslib-1.19/sam.c:2651:19: note: Shadow variable
htslib-1.19/sam.c:2832:43: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/sam.c:2733:9: note: Shadowed declaration
htslib-1.19/sam.c:2832:43: note: Shadow variable
htslib-1.19/sam.c:4092:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.19/sam.c:4078:9: note: Shadowed declaration
htslib-1.19/sam.c:4092:17: note: Shadow variable
htslib-1.19/sam.c:4264:18: style: Local variable 's' shadows outer variable [shadowVariable]
htslib-1.19/sam.c:4233:14: note: Shadowed declaration
htslib-1.19/sam.c:4264:18: note: Shadow variable
htslib-1.19/sam.c:5448:25: style: Local variable 'j' shadows outer variable [shadowVariable]
htslib-1.19/sam.c:5388:9: note: Shadowed declaration
htslib-1.19/sam.c:5448:25: note: Shadow variable
htslib-1.19/sam.c:346:11: style: Variable 'text' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:395:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:676:14: style: Variable 'CG' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:1176:14: style: Variable 'hb' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:1186:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:1276:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:1404:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:1579:17: style: Variable 's' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:1604:11: style: Variable 'fd' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:2031:19: style: Variable 'tab' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:2217:15: style: Variable 'text' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:2291:19: style: Variable 'beg' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:2291:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:2301:18: style: Variable 'tmp' can be declared as const array [constVariable]
htslib-1.19/sam.c:2546:43: style: Parameter 'tag_whitelist' can be declared as pointer to const [constParameterPointer]
htslib-1.19/sam.c:2550:23: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:2732:22: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:2783:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:3337:34: 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-1.19/sam.c:3473:42: note: You might need to cast the function pointer here
htslib-1.19/sam.c:3337:34: note: Parameter 'arg' can be declared as pointer to const
htslib-1.19/sam.c:3426:19: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:3680:14: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:3874:15: style: Variable 'bc' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:3922:11: style: Variable 'name' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4052:57: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/sam.c:4193:26: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4233:14: style: Variable 's' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4233:18: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4248:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4559:22: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4695:14: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4720:22: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4768:39: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:4915:62: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
htslib-1.19/sam.c:5084:11: style: Variable 'opts' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:5283:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:5284:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:5389:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:5678:14: style: Variable 'a_seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:5678:40: style: Variable 'b_seq' can be declared as pointer to const [constVariablePointer]
htslib-1.19/sam.c:1069:32: 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]
htslib-1.19/sam.c:61:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.19/test/test_bgzf.c:518:56: warning: Either the condition 'pos<sizeof(append_mode)-1' is redundant or the array 'mode[2]' is accessed at index 14, which is out of bounds. [arrayIndexOutOfBoundsCond]
htslib-1.19/test/test_bgzf.c:518:23: note: Assuming that condition 'pos<sizeof(append_mode)-1' is not redundant
htslib-1.19/test/test_bgzf.c:518:56: note: Array index out of bounds
htslib-1.19/test/test_bgzf.c:519:32: error: Array 'mode[2]' accessed at index 14, which is out of bounds. [arrayIndexOutOfBounds]
htslib-1.19/test/test_bgzf.c:497:9: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
htslib-1.19/test/test_bgzf.c:570:9: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
htslib-1.19/test/test_bgzf.c:570:9: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
htslib-1.19/test/test_bgzf.c:255:36: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:435:35: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:511:34: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:622:33: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:638:41: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:730:39: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:831:34: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:881:37: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_bgzf.c:938:55: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_expr.c:307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:91:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:104:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:275:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:300:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:325:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:355:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:382:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_faidx.c:445:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_expr.c:101:19: warning: Either the condition 'a' is redundant or there is possible null pointer dereference: a. [nullPointerRedundantCheck]
htslib-1.19/test/test_expr.c:100:9: note: Assuming that condition 'a' is not redundant
htslib-1.19/test/test_expr.c:101:19: note: Null pointer dereference
htslib-1.19/test/test_index.c:39:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_index.c:49:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kfunc.c:43:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kfunc.c:84:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:51:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:102:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:134:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:200:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:314:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:370:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:392:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_mod.c:120:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_kstring.c:50:13: style: Condition 'val!=0' is always false [knownConditionTrueFalse]
htslib-1.19/test/test_kstring.c:45:11: note: Assignment 'val=0', assigned value is 0
htslib-1.19/test/test_kstring.c:50:13: note: Condition 'val!=0' is always false
htslib-1.19/test/test_kstring.c:380:11: style: Variable 'test' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test_realn.c:39:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_realn.c:60:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_mod.c:173:14: style: Variable 'all_mods' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test_str2int.c:53:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_str2int.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_str2int.c:160:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_str2int.c:166:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_str2int.c:200:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_str2int.c:217:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_realn.c:45:11: style: Variable 'in_name' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test_realn.c:46:11: style: Variable 'out_name' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test_realn.c:47:11: style: Variable 'ref_name' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test_realn.c:49:10: style: Variable 'modew' can be declared as const array [constVariable]
htslib-1.19/hts_time_funcs.h:168:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_time_funcs.c:44:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_time_funcs.c:58:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/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-1.19/test/thrash_threads1.c:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/thrash_threads3.c:38:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/thrash_threads4.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/thrash_threads4.c:57:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/test/thrash_threads4.c:61:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/test/thrash_threads5.c:40:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/thrash_threads6.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/thrash_threads6.c:94:17: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/test/thrash_threads7.c:87:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/thrash_threads7.c:45:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.19/test/thrash_threads7.c:44:19: style: Variable 'usecs' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test_view.c:73:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_view.c:212:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.19/test/test_view.c:306:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.19/hts.c:1264:21: style: Redundant condition: The condition '*str' is redundant since '*str == ','' is sufficient. [redundantCondition]
htslib-1.19/hts.c:1140:41: style: Condition 'strcmp(o->arg,"store_md")==0' is always false [knownConditionTrueFalse]
htslib-1.19/hts.c:1144:41: style: Condition 'strcmp(o->arg,"store_nm")==0' is always false [knownConditionTrueFalse]
htslib-1.19/hts.c:2470:64: style: Condition 'tid<0' is always false [knownConditionTrueFalse]
htslib-1.19/hts.c:2470:52: note: Assuming that condition 'idx->z.last_tid>=0' is not redundant
htslib-1.19/hts.c:2470:25: note: Assuming that condition 'idx->z.last_tid!=tid' is not redundant
htslib-1.19/hts.c:2470:64: note: Condition 'tid<0' is always false
htslib-1.19/hts.c:2610:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/hts.c:2610:18: note: Calling function 'ed_is_big' returns 0
htslib-1.19/hts.c:2610:18: note: Condition 'ed_is_big()' is always false
htslib-1.19/hts.c:2616:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/hts.c:2616:18: note: Calling function 'ed_is_big' returns 0
htslib-1.19/hts.c:2616:18: note: Condition 'ed_is_big()' is always false
htslib-1.19/hts.c:2622:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.19/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1
htslib-1.19/hts.c:2622:18: note: Calling function 'ed_is_big' returns 0
htslib-1.19/hts.c:2622:18: note: Condition 'ed_is_big()' is always false
htslib-1.19/hts.c:2794:22: style: Condition 'l->n<0' is always false [knownConditionTrueFalse]
htslib-1.19/hts.c:2793:20: note: Assignment 'l->n=x', assigned value is greater than -1
htslib-1.19/hts.c:2794:22: note: Condition 'l->n<0' is always false
htslib-1.19/hts.c:4131:53: style: Condition 'iter->end>beg' is always true [knownConditionTrueFalse]
htslib-1.19/hts.c:4129:41: note: Assuming that condition 'beg>=iter->end' is not redundant
htslib-1.19/hts.c:4131:53: note: Condition 'iter->end>beg' is always true
htslib-1.19/hts.c:4268:32: style: Condition 'iter->i<iter->n_off' is always true [knownConditionTrueFalse]
htslib-1.19/hts.c:4235:25: note: Assuming that condition 'iter->i>=iter->n_off' is not redundant
htslib-1.19/hts.c:4268:32: note: Condition 'iter->i<iter->n_off' is always true
htslib-1.19/hts.c:1139:46: style: Same expression on both sides of '||'. [duplicateExpression]
htslib-1.19/hts.c:1143:46: style: Same expression on both sides of '||'. [duplicateExpression]
htslib-1.19/hts.c:1408:48: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.19/hts.c:527:30: style:inconclusive: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:544:37: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.19/hts.c:527:30: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.19/hts.c:532:31: style:inconclusive: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:561:38: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.19/hts.c:532:31: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.19/hts.c:1258:35: style:inconclusive: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:452:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'.
htslib-1.19/hts.c:1258:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'.
htslib-1.19/hts.c:1295:33: style:inconclusive: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:438:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'.
htslib-1.19/hts.c:1295:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'.
htslib-1.19/hts.c:1421:27: style:inconclusive: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:629:34: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.19/hts.c:1421:27: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.19/hts.c:1996:33: style:inconclusive: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:696:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'.
htslib-1.19/hts.c:1996:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'.
htslib-1.19/hts.c:3978:41: style:inconclusive: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:1180:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'.
htslib-1.19/hts.c:3978:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'.
htslib-1.19/hts.c:3998:39: style:inconclusive: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent]
htslib-1.19/htslib/hts.h:1190:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'.
htslib-1.19/hts.c:3998:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'.
htslib-1.19/hts.c:603:15: style: Local variable 's' shadows outer variable [shadowVariable]
htslib-1.19/hts.c:535:19: note: Shadowed declaration
htslib-1.19/hts.c:603:15: note: Shadow variable
htslib-1.19/hts.c:2789:17: style: Local variable 'j' shadows outer variable [shadowVariable]
htslib-1.19/hts.c:2760:13: note: Shadowed declaration
htslib-1.19/hts.c:2789:17: note: Shadow variable
htslib-1.19/hts.c:3121:21: style: Local variable 'bin' shadows outer variable [shadowVariable]
htslib-1.19/hts.c:3114:19: note: Shadowed declaration
htslib-1.19/hts.c:3121:21: note: Shadow variable
htslib-1.19/hts.c:3272:22: style: Local variable 'off' shadows outer variable [shadowVariable]
htslib-1.19/hts.c:3255:23: note: Shadowed declaration
htslib-1.19/hts.c:3272:22: note: Shadow variable
htslib-1.19/hts.c:4243:36: style: Local variable 'r' shadows outer argument [shadowArgument]
htslib-1.19/hts.c:4143:60: note: Shadowed declaration
htslib-1.19/hts.c:4243:36: note: Shadow variable
htslib-1.19/hts.c:4298:40: style: Local variable 'r' shadows outer argument [shadowArgument]
htslib-1.19/hts.c:4143:60: note: Shadowed declaration
htslib-1.19/hts.c:4298:40: note: Shadow variable
htslib-1.19/hts.c:4314:33: style: Local variable 'tid' shadows outer variable [shadowVariable]
htslib-1.19/hts.c:4146:14: note: Shadowed declaration
htslib-1.19/hts.c:4314:33: note: Shadow variable
htslib-1.19/hts.c:4315:37: style: Local variable 'end' shadows outer variable [shadowVariable]
htslib-1.19/hts.c:4147:20: note: Shadowed declaration
htslib-1.19/hts.c:4315:37: note: Shadow variable
htslib-1.19/hts.c:136:43: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/hts.c:138:38: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/hts.c:140:39: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/hts.c:142:46: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/hts.c:144:41: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/hts.c:146:40: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.19/hts.c:1208:14: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:1426:34: style: Variable 'opts' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:1821:15: style: Variable 'expr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:2425:36: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hts.c:2601:28: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hts.c:2659:17: style: Variable 'lidx' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:2667:29: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:2910:38: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hts.c:2928:17: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:2973:112: style: Parameter 'bidx' can be declared as pointer to const [constParameterPointer]
htslib-1.19/hts.c:3135:13: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:3188:20: style: Variable 'reg1' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:3189:20: style: Variable 'reg2' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:3474:31: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:3571:19: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:4148:20: style: Variable 'found_reg' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:4567:11: style: Variable 'csi_ext' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:4568:11: style: Variable 'bai_ext' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:4569:11: style: Variable 'tbi_ext' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:4570:11: style: Variable 'crai_ext' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:4571:11: style: Variable 'fai_ext' can be declared as pointer to const [constVariablePointer]
htslib-1.19/hts.c:4391:50: error: Uninitialized variables: &key.reg, &key.intervals, &key.count, &key.min_beg, &key.max_end [uninitvar]
htslib-1.19/hts.c:3260:23: style: Variable 'unmapped' is assigned a value that is never used. [unreadVariable]
htslib-1.19/hts.c:4237:32: style: Variable 'next_range' is assigned a value that is never used. [unreadVariable]
htslib-1.19/htslib/kstring.h:160:12: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/hts.h:1544:16: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/hts.h:1552:6: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/hts.h:1562:6: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/hts.h:1573:6: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/sam.h:1470:18: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/sam.h:1478:21: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/sam.h:1566:29: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/sam.h:1574:30: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/kbitset.h:82:4: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/kbitset.h:106:9: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:30:1: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:46:31: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:55:31: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:59:37: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:68:31: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:80:31: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:100:31: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:118:31: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash_str2int.h:131:31: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1120:36: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1536:22: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1544:18: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1576:18: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1623:14: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1626:14: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1629:14: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1632:14: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/vcf.h:1664:14: style: C-style pointer casting [cstyleCast]
htslib-1.19/test/usepublic.cpp:61:1: style: C-style pointer casting [cstyleCast]
htslib-1.19/test/usepublic.cpp:64:1: style: C-style pointer casting [cstyleCast]
htslib-1.19/test/usepublic.cpp:66:1: style: C-style pointer casting [cstyleCast]
htslib-1.19/test/usepublic.cpp:70:1: style: C-style pointer casting [cstyleCast]
htslib-1.19/htslib/khash.h:421:64: performance: Function parameter 'ks' should be passed by const reference. [passedByValue]
htslib-1.19/test/usepublic.cpp:70:1: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/usepublic.cpp:61:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.19/textutils.c:169:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/textutils.c:327:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.19/textutils.c:455:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.19/thread_pool.c:752:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_RECURSIVE [valueFlowBailoutIncompleteVar]
htslib-1.19/thread_pool.c:856:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.19/textutils.c:185:23: style: Variable 'lim' can be declared as pointer to const [constVariablePointer]
htslib-1.19/textutils.c:202:40: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
htslib-1.19/textutils.c:228:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
htslib-1.19/textutils.c:238:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
htslib-1.19/textutils.c:456:21: style: Variable 'bufend' can be declared as pointer to const [constVariablePointer]
htslib-1.19/thread_pool.c:1048:36: style: Condition 'hts_tpool_process_flush(q)!=0' is always false [knownConditionTrueFalse]
htslib-1.19/thread_pool.c:1048:32: note: Calling function 'hts_tpool_process_flush' returns 0
htslib-1.19/thread_pool.c:1048:36: note: Condition 'hts_tpool_process_flush(q)!=0' is always false
htslib-1.19/thread_pool.c:354:47: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
htslib-1.19/thread_pool.c:473:43: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
htslib-1.19/thread_pool.c:815:31: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
htslib-1.19/thread_pool.c:1077:48: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf_sweep.c:82:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf_sweep.c:106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf_sweep.c:174:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf_sweep.c:58:45: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf_sweep.c:189:39: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer]
htslib-1.19/test/test_view.c:286:11: style: Variable 'out_fn' can be declared as pointer to const [constVariablePointer]
htslib-1.19/test/test_view.c:200:29: style: Variable 'r' is assigned a value that is never used. [unreadVariable]
htslib-1.19/vcf.c:601:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition]
htslib-1.19/vcf.c:610:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition]
htslib-1.19/vcf.c:616:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition]
htslib-1.19/vcfutils.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcfutils.c:216:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcfutils.c:286:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.19/vcf.c:1972:78: style: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false [knownConditionTrueFalse]
htslib-1.19/vcf.c:1972:26: note: Calling function 'bcf_enc_vchar' returns 0
htslib-1.19/vcf.c:1972:78: note: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false
htslib-1.19/vcf.c:3326:16: style: Condition 'ret' is always true [knownConditionTrueFalse]
htslib-1.19/vcf.c:3165:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcf.c:3233:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcf.c:3266:43: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcf.c:3592:32: portability: Casting between signed int * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcf.c:5817:52: style: Same value in both branches of ternary operator. [duplicateValueTernary]
htslib-1.19/vcf.c:183:35: style:inconclusive: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:571:39: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.19/vcf.c:183:35: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.19/vcf.c:183:50: style:inconclusive: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:571:56: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'.
htslib-1.19/vcf.c:183:50: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'.
htslib-1.19/vcf.c:1264:31: style:inconclusive: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:596:35: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.19/vcf.c:1264:31: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.19/vcf.c:1274:32: style:inconclusive: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:620:36: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.19/vcf.c:1274:32: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.19/vcf.c:1339:31: style:inconclusive: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:599:35: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.19/vcf.c:1339:31: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.19/vcf.c:1339:48: style:inconclusive: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:599:50: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'.
htslib-1.19/vcf.c:1339:48: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'.
htslib-1.19/vcf.c:1472:34: style:inconclusive: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:340:38: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/vcf.c:1472:34: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/vcf.c:1529:28: style:inconclusive: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:376:32: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/vcf.c:1529:28: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/vcf.c:1948:45: style:inconclusive: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:506:49: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'.
htslib-1.19/vcf.c:1948:45: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'.
htslib-1.19/vcf.c:2190:24: style:inconclusive: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:452:28: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/vcf.c:2190:24: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.19/vcf.c:2447:56: style:inconclusive: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:645:60: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'.
htslib-1.19/vcf.c:2447:56: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'.
htslib-1.19/vcf.c:4237:37: style:inconclusive: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:1202:41: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.19/vcf.c:4237:37: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.19/vcf.c:4237:44: style:inconclusive: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:1202:50: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'.
htslib-1.19/vcf.c:4237:44: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'.
htslib-1.19/vcf.c:4614:73: style:inconclusive: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcf.h:790:77: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'.
htslib-1.19/vcf.c:4614:73: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'.
htslib-1.19/vcf.c:767:17: style: Local variable 'k' shadows outer variable [shadowVariable]
htslib-1.19/vcf.c:742:13: note: Shadowed declaration
htslib-1.19/vcf.c:767:17: note: Shadow variable
htslib-1.19/vcf.c:3026:13: style: Local variable 'j' shadows outer variable [shadowVariable]
htslib-1.19/vcf.c:2982:9: note: Shadowed declaration
htslib-1.19/vcf.c:3026:13: note: Shadow variable
htslib-1.19/vcf.c:4100:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/vcf.c:3935:9: note: Shadowed declaration
htslib-1.19/vcf.c:4100:13: note: Shadow variable
htslib-1.19/vcf.c:4873:16: style: Local variable 'samples' shadows outer argument [shadowArgument]
htslib-1.19/vcf.c:4814:53: note: Shadowed declaration
htslib-1.19/vcf.c:4873:16: note: Shadow variable
htslib-1.19/vcf.c:4902:17: style: Local variable 'k' shadows outer variable [shadowVariable]
htslib-1.19/vcf.c:4875:13: note: Shadowed declaration
htslib-1.19/vcf.c:4902:17: note: Shadow variable
htslib-1.19/vcf.c:275:38: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:329:34: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:426:35: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:512:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:522:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:533:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:945:50: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:986:36: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:1159:38: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:1371:17: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:1414:20: style: Variable 'dsize' can be declared as const array [constVariable]
htslib-1.19/vcf.c:1672:57: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:1728:64: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:1825:19: style: Variable 'id_tmp' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:1958:40: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:1994:21: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:2014:11: style: Variable 'shared_ori' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:2116:24: style: Variable 'fmt' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:2302:23: style: Variable 'tab' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:2338:25: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:2514:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:2642:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:2730:19: style: Variable 'p_end' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:2817:47: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:2890:45: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:2915:21: style: Variable 'meta' can be declared as const array [constVariable]
htslib-1.19/vcf.c:2927:15: style: Variable 'r_start' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:3035:46: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:3620:23: style: Variable 't' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4026:27: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4073:29: style: Variable 'missing' can be declared as const array [constVariable]
htslib-1.19/vcf.c:4134:31: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4205:56: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:4373:49: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:4476:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4489:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4498:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4499:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4569:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4582:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4591:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4592:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4922:59: style: Parameter 'imap' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:4933:24: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:5450:62: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
htslib-1.19/vcf.c:5774:18: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcf.c:4400:35: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
htslib-1.19/vcf.c:1008:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
htslib-1.19/vcf.c:1388:14: style: Variable 'hrec' is assigned a value that is never used. [unreadVariable]
htslib-1.19/vcfutils.c:463:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcfutils.c:497:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcfutils.c:775:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcfutils.c:829:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.19/vcf.c:2516:17: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
htslib-1.19/vcf.c:2516:34: style: Variable 'min' is assigned a value that is never used. [unreadVariable]
htslib-1.19/vcf.c:3385:22: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
htslib-1.19/vcf.c:3409:19: style: Variable 'max_n_flt' is assigned a value that is never used. [unreadVariable]
htslib-1.19/vcfutils.c:134:55: style:inconclusive: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcfutils.h:117:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'.
htslib-1.19/vcfutils.c:134:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'.
htslib-1.19/vcfutils.c:134:66: style:inconclusive: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcfutils.h:117:65: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'.
htslib-1.19/vcfutils.c:134:66: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'.
htslib-1.19/vcfutils.c:241:67: style:inconclusive: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. [funcArgNamesDifferent]
htslib-1.19/htslib/vcfutils.h:61:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'.
htslib-1.19/vcfutils.c:241:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'.
htslib-1.19/vcfutils.c:43:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/vcfutils.c:34:9: note: Shadowed declaration
htslib-1.19/vcfutils.c:43:13: note: Shadow variable
htslib-1.19/vcfutils.c:96:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.19/vcfutils.c:34:9: note: Shadowed declaration
htslib-1.19/vcfutils.c:96:13: note: Shadow variable
htslib-1.19/vcfutils.c:579:17: style: Local variable 'size' shadows outer variable [shadowVariable]
htslib-1.19/vcfutils.c:563:13: note: Shadowed declaration
htslib-1.19/vcfutils.c:579:17: note: Shadow variable
htslib-1.19/vcfutils.c:44:18: style: Variable 'ac_ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:462:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:463:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:496:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:497:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:624:56: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:774:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:775:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:828:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
htslib-1.19/vcfutils.c:829:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
diff:
head htslib-1.19/annot-tsv.c:120:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head htslib-1.19/annot-tsv.c:305:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/annot-tsv.c:873:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/bcf_sr_sort.c:219:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/bcf_sr_sort.c:240:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/bcf_sr_sort.c:306:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/bcf_sr_sort.c:325:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/bcf_sr_sort.c:332:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/bcf_sr_sort.c:375:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:1029:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:1543:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:1840:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:2375:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:2406:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:2473:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:2513:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:333:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:368:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:409:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:478:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:505:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:527:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:543:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzf.c:919:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzip.c:102:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzip.c:165:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzip.c:52:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzip.c:60:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
head htslib-1.19/bgzip.c:67:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/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-1.19/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1003:35: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1003:54: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1004:29: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/cram/cram_codecs.c:1456:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_codecs.c:1641:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_codecs.c:1661:60: error: Shifting signed 32-bit value by 31 bits is undefined behaviour [shiftTooManyBitsSigned]
2.13.0 htslib-1.19/cram/cram_codecs.c:1661:60: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
head htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1667:41: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1667:60: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1667:75: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1667:85: note: Parameter 'out' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1667:95: note: Parameter 'out_size' can be declared as pointer to const
head htslib-1.19/cram/cram_codecs.c:1688:55: style: Parameter 'slice' can be declared as pointer to const [constParameterPointer]
head htslib-1.19/cram/cram_codecs.c:1688:74: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
head htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1692:41: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1692:60: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1692:75: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1692:85: note: Parameter 'out' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1692:95: note: Parameter 'out_size' can be declared as pointer to const
head htslib-1.19/cram/cram_codecs.c:1734:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_codecs.c:1810:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/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-1.19/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1949:41: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1949:60: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1950:34: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1954:40: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1954:59: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:1955:33: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2046:39: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2046:58: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2046:73: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2046:83: note: Parameter 'out' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2046:93: note: Parameter 'out_size' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2051:38: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2051:57: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2051:72: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2051:82: note: Parameter 'out' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2051:92: note: Parameter 'out_size' can be declared as pointer to const
head htslib-1.19/cram/cram_codecs.c:2187:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/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-1.19/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2341:39: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2341:58: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2342:34: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2347:38: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2347:57: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2348:33: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2623:42: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2623:61: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2624:42: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2624:52: note: Parameter 'out' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2624:62: note: Parameter 'out_size' can be declared as pointer to const
head htslib-1.19/cram/cram_codecs.c:2781:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_codecs.c:2820:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/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-1.19/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2971:43: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2971:62: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:2972:37: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:3007:42: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:3007:61: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:3008:36: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:3044:43: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:3044:62: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:3045:37: note: Parameter 'in' can be declared as pointer to const
head htslib-1.19/cram/cram_codecs.c:753:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_codecs.c:801:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/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-1.19/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:960:40: note: Parameter 'slice' can be declared as pointer to const
head htslib-1.19/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-1.19/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here
     htslib-1.19/cram/cram_codecs.c:960:59: note: Parameter 'c' can be declared as pointer to const
head htslib-1.19/cram/cram_codecs.c:965:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_codecs.c:995:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_decode.c:175:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_decode.c:2340:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_decode.c:2972:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_encode.c:1246:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
head htslib-1.19/cram/cram_encode.c:1258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_encode.c:3257:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_encode.c:4140:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_external.c:520:58: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
head htslib-1.19/cram/cram_external.c:609:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RANS_ORDER_X32 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_index.c:666:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_index.c:704:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_index.c:741:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_index.c:832:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId32 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:1512:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:1805:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fqz_slice [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:2475:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:2508:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:2685:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:2846:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:2964:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:3877:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:4310:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:4857:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:4971:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:5703:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_io.c:5996:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/cram_stats.c:95:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/mFILE.c:182:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/mFILE.c:198:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/mFILE.c:463:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/cram/open_trace_file.c:195:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/errmod.c:34:1: style: Parameter 'array' can be declared as const array [constParameter]
2.13.0 htslib-1.19/errmod.c:34:1: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
2.13.0 htslib-1.19/errmod.c:34:1: style: Variable 'ea' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/errmod.c:34:1: style: Variable 'eb' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/errmod.c:34:1: style: Variable 'j' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/errmod.c:34:1: style: Variable 'k' can be declared as pointer to const [constVariablePointer]
head htslib-1.19/errmod.c:93:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
head htslib-1.19/faidx.c:341:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/faidx.c:384:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SCNu64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/faidx.c:496:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/faidx.c:586:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/faidx.c:699:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/faidx.c:83:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:1070:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:1101:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:1209:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:189:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:1936:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:1967:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:735:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/header.c:767:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SSIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:1033:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:1135:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:157:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:187:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:230:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:240:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:286:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:320:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:360:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:371:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:382:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:406:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:422:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:443:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:488:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:501:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:543:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:554:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:586:28: 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-1.19/hfile.c:624:33: note: You might need to cast the function pointer here
     htslib-1.19/hfile.c:586:28: note: Parameter 'fpv' can be declared as pointer to const
head htslib-1.19/hfile.c:599:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:618:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:654:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:725:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:753:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:784:30: 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-1.19/hfile.c:797:17: note: You might need to cast the function pointer here
     htslib-1.19/hfile.c:784:30: note: Parameter 'fpv' can be declared as pointer to const
head htslib-1.19/hfile.c:786:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:790:29: style: Parameter 'fpv' can be declared as pointer to const [constParameterPointer]
head htslib-1.19/hfile.c:824:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:870:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:891:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hopenv_mem [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile.c:919:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_gcs.c:145:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gcs_vopen [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_gcs.c:75:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:1016:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:1134:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:1188:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:131:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOSYS [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:1436:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:1505:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vhopen_libcurl [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:160:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:240:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EBADF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:282:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:315:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:329:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:370:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:513:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:568:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:701:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLM_OK [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:750:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_WRITEFUNC_PAUSE [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:767:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:826:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:870:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_READFUNC_PAUSE [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:889:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_libcurl.c:934:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:157:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:170:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:216:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:256:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_CUSTOMREQUEST [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:322:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_POST [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:404:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_UPLOAD [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:440:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:506:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLINFO_RESPONSE_CODE [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:572:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:613:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_URL [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:649:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:682:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:779:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:804:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:826:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar]
head htslib-1.19/hfile_s3_write.c:839:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vhopen_s3_write [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/hts.c:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head htslib-1.19/hts.c:1457:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:152:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_CC [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:1644:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:1937:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:1979:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2011:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2070:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2160:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/hts.c:2160:1: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
2.13.0 htslib-1.19/hts.c:2160:1: style: Variable 'ea' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/hts.c:2160:1: style: Variable 'eb' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/hts.c:2160:1: style: Variable 'j' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/hts.c:2160:1: style: Variable 'k' can be declared as pointer to const [constVariablePointer]
head htslib-1.19/hts.c:2161:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/hts.c:2161:1: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
2.13.0 htslib-1.19/hts.c:2161:1: style: Variable 'ea' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/hts.c:2161:1: style: Variable 'eb' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/hts.c:2161:1: style: Variable 'j' can be declared as pointer to const [constVariablePointer]
2.13.0 htslib-1.19/hts.c:2161:1: style: Variable 'k' can be declared as pointer to const [constVariablePointer]
head htslib-1.19/hts.c:2432:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2484:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2699:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2781:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2832:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:2894:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:3031:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:3265:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:3629:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4003:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4097:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4161:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4494:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4728:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4814:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4850:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4911:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:4987:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/hts.c:700:18: style: Condition 'len>=1' is always true [knownConditionTrueFalse]
     htslib-1.19/hts.c:592:13: note: Assuming that condition 'len==0' is not redundant
     htslib-1.19/hts.c:700:18: note: Condition 'len>=1' is always true
2.13.0 htslib-1.19/hts.c:705:18: style: Condition 'len>=1' is always true [knownConditionTrueFalse]
     htslib-1.19/hts.c:592:13: note: Assuming that condition 'len==0' is not redundant
     htslib-1.19/hts.c:705:18: note: Condition 'len>=1' is always true
head htslib-1.19/hts.c:86:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_VERSION_TEXT [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts.c:949:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts_expr.c:268:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts_expr.c:292:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts_expr.c:751:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REG_EXTENDED [valueFlowBailoutIncompleteVar]
head htslib-1.19/hts_expr.c:879:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/htsfile.c:116:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/htsfile.c:155:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htsfile.c:257:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head htslib-1.19/htsfile.c:51:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/htsfile.c:72:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/hts_expr.h:80:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:238:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:247:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:263:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:272:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:313:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:369:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/kstring.h:385:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/sam.h:1628:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/sam.h:1699:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/vcf.h:1213:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
head htslib-1.19/htslib/vcf.h:1316:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/kstring.c:277:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/kstring.c:310:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/kstring.c:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/multipart.c:114:39: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'multipart_write' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     htslib-1.19/multipart.c:140:21: note: You might need to cast the function pointer here
     htslib-1.19/multipart.c:114:39: note: Parameter 'fpv' can be declared as pointer to const
head htslib-1.19/multipart.c:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/multipart.c:120:36: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'multipart_seek' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     htslib-1.19/multipart.c:140:38: note: You might need to cast the function pointer here
     htslib-1.19/multipart.c:120:36: note: Parameter 'fpv' can be declared as pointer to const
head htslib-1.19/multipart.c:122:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/multipart.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/multipart.c:259:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/plugin.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/plugin.c:190:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/plugin.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/plugin.c:77:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUGIN_EXT [valueFlowBailoutIncompleteVar]
head htslib-1.19/probaln.c:86:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/realn.c:216:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/realn.c:94:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/regidx.c:164:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:1092:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:1863:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:2157:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:2188:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:2323:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:2732:22: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
head htslib-1.19/sam.c:2766:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:3166:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EIO [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:3263:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:3337:34: 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-1.19/sam.c:3473:42: note: You might need to cast the function pointer here
     htslib-1.19/sam.c:3337:34: note: Parameter 'arg' can be declared as pointer to const
head htslib-1.19/sam.c:3418:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:3529:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:3693:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4057:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4094:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4204:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4303:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4328:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:436:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4539:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4652:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4696:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4705:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4732:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4739:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4749:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4766:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4818:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4887:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4922:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:4980:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:5006:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:5015:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:5022:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:5032:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:5042:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:554:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:5682:29: style: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value. [duplicateExpression]
     htslib-1.19/sam.c:5680:31: note: 'iref' is assigned value 'b->core.pos' here.
     htslib-1.19/sam.c:5682:29: note: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value.
2.13.0 htslib-1.19/sam.c:5682:29: style: Same expression on both sides of '-'. [duplicateExpression]
     htslib-1.19/sam.c:5680:31: note: 'iref' is assigned value 'b->core.pos' here.
     htslib-1.19/sam.c:5682:29: note: Same expression on both sides of '-'.
head htslib-1.19/sam.c:5895:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:5994:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:6128:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:683:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:832:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam.c:913:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/sam.c:972:28: 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]
head htslib-1.19/sam.c:980:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/sam_internal.h:56:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/add_header.c:52:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/add_header.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/cram.c:57:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/cram.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/dump_aux.c:126:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/dump_aux.c:96:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/flags_demo.c:53:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/flags_demo.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/flags_htsopt_field.c:53:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/flags_htsopt_field.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/index_multireg_read.c:54:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/index_multireg_read.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/index_reg_read.c:59:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/index_reg_read.c:68:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/index_write.c:54:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/index_write.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/mod_aux.c:53:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/mod_aux.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/mod_aux_ba.c:52:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/mod_aux_ba.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/mod_bam.c:53:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/mod_bam.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/modstate.c:52:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/modstate.c:64:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/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-1.19/samples/mpileup.c:138:36: note: You might need to cast the function pointer here
     htslib-1.19/samples/mpileup.c:56:26: note: Parameter 'data' can be declared as pointer to const
head htslib-1.19/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-1.19/samples/mpileup.c:138:36: note: You might need to cast the function pointer here
     htslib-1.19/samples/mpileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const
head htslib-1.19/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-1.19/samples/mpileup.c:139:35: note: You might need to cast the function pointer here
     htslib-1.19/samples/mpileup.c:60:25: note: Parameter 'data' can be declared as pointer to const
head htslib-1.19/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-1.19/samples/mpileup.c:139:35: note: You might need to cast the function pointer here
     htslib-1.19/samples/mpileup.c:60:63: note: Parameter 'cd' can be declared as pointer to const
2.13.0 htslib-1.19/samples/mpileup.c:86:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/mpileup.c:96:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/pileup.c:104:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/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-1.19/samples/pileup.c:131:34: note: You might need to cast the function pointer here
     htslib-1.19/samples/pileup.c:56:26: note: Parameter 'data' can be declared as pointer to const
head htslib-1.19/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-1.19/samples/pileup.c:131:34: note: You might need to cast the function pointer here
     htslib-1.19/samples/pileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const
head htslib-1.19/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-1.19/samples/pileup.c:132:33: note: You might need to cast the function pointer here
     htslib-1.19/samples/pileup.c:65:25: note: Parameter 'data' can be declared as pointer to const
head htslib-1.19/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-1.19/samples/pileup.c:132:33: note: You might need to cast the function pointer here
     htslib-1.19/samples/pileup.c:65:63: note: Parameter 'cd' can be declared as pointer to const
2.13.0 htslib-1.19/samples/pileup.c:94:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/pileup_mod.c:100:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/pileup_mod.c:109:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/read_aux.c:122:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/read_aux.c:96:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/read_bam.c:51:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/read_bam.c:63:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/read_fast.c:52:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/read_fast.c:58:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/read_header.c:53:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/read_header.c:56:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/read_refname.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
2.13.0 htslib-1.19/samples/read_refname.c:52:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/read_refname.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/rem_header.c:53:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/rem_header.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/split.c:54:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/split.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/split2.c:54:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/split2.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/split_thread1.c:54:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/split_thread1.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/split_thread2.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/split_thread2.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/update_header.c:53:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/update_header.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/samples/write_fast.c:52:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/samples/write_fast.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:126:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pair [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:1433:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:201:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:220:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable targets_overlap [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:412:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:447:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:455:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:512:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:668:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:761:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:859:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:86:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/synced_bcf_reader.c:989:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/tabix.c:110:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/tabix.c:163:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/tabix.c:413:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/tabix.c:534:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/tabix.c:59:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head htslib-1.19/tabix.c:71:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/tbx.c:162:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/tbx.c:439:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/fieldarith.c:42:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hfile.c:107:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hfile.c:40:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hfile.c:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hts_endian.c:252:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hts_endian.c:333:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hts_endian.c:415:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hts_endian.c:460:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/hts_endian.c:508:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/pileup.c:135:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/pileup.c:180:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/pileup.c:216:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/test/plugins-dlhts.c:183:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:1064:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:112:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:1170:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:1228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:1397:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:1516:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:156:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:1581:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:1783:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2005:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2041:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2086:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2115:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2137:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:213:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2154:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2174:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2203:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2243:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:2315:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:318:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:64:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:901:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/sam.c:992:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-bcf-sr.c:145:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-bcf-sr.c:47:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-bcf-sr.c:54:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-bcf-translate.c:114:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-bcf-translate.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-bcf_set_variant_type.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-parse-reg.c:172:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-parse-reg.c:63:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-parse-reg.c:98:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:128:103: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:162:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:193:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:218:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu32 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:281:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:363:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:417:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:441:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:50:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:60:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-regidx.c:69:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:112:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:288:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:407:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:435:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:493:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:52:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:547:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-api.c:586:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test-vcf-sweep.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:1035:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:113:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:125:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:168:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:184:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:194:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:207:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:218:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:238:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:248:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:270:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:281:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:291:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:302:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:318:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:332:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:367:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:408:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:444:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:524:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:590:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:623:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:646:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:71:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:741:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:81:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:842:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:881:37: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
head htslib-1.19/test/test_bgzf.c:888:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:938:55: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
head htslib-1.19/test/test_bgzf.c:93:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_bgzf.c:949:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_expr.c:307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:104:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:275:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:300:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:325:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:355:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:382:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:445:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_faidx.c:91:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_index.c:39:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_index.c:49:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kfunc.c:84:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kstring.c:102:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kstring.c:134:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kstring.c:200:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kstring.c:314:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kstring.c:370:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kstring.c:392:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_kstring.c:51:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_mod.c:120:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_realn.c:39:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_realn.c:60:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_str2int.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_str2int.c:160:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_str2int.c:166:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_str2int.c:200:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_str2int.c:217:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_str2int.c:53:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_time_funcs.c:44:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_time_funcs.c:58:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_view.c:212:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_view.c:306:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/test_view.c:73:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
2.13.0 htslib-1.19/test/thrash_threads7.c:60:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_FAILURE [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/thrash_threads7.c:87:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/test/usepublic.cpp:70:1: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
2.13.0 htslib-1.19/test/usepublic.cpp:70:1: style: Variable 'sep' can be declared as pointer to const [constVariablePointer]
head htslib-1.19/textutils.c:169:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/textutils.c:327:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head htslib-1.19/textutils.c:455:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/thread_pool.c:856:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:1166:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:1216:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:1511:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:1532:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:1731:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:1760:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:1910:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2197:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2267:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2384:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:242:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2467:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2822:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2848:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2956:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:2992:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:3066:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:313:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:3295:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:336:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:3431:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:3490:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:351:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:377:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:3884:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:3941:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:4260:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:4620:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:4794:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5071:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5082:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5145:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5304:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5411:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5432:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5454:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5470:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5626:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5633:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5663:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5747:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:5786:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf.c:710:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf_sweep.c:106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf_sweep.c:174:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcf_sweep.c:82:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcfutils.c:216:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcfutils.c:286:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
head htslib-1.19/vcfutils.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]


DONE