2025-05-05 00:14
ftp://ftp.de.debian.org/debian/pool/main/h/htslib/htslib_1.21+ds.orig.tar.bz2
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib --library=libcurl --library=openssl  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-1022-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: 88ef81e (2025-05-02 08:42:38 +0200)
count: 1544 1529
elapsed-time: 32.5 31.8
head-timing-info:

old-timing-info:

head results:
htslib-1.21/htslib/kstring.h:159:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:238:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:247:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:263:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:272:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:313:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:369:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/kstring.h:381:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/annot-tsv.c:122:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/annot-tsv.c:307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/annot-tsv.c:960:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/vcf.h:1214:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/vcf.h:1317:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bcf_sr_sort.c:219:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/bcf_sr_sort.c:240:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/bcf_sr_sort.c:306:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/bcf_sr_sort.c:325:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/bcf_sr_sort.c:332:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/bcf_sr_sort.c:375:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/hfile.h:285:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bufsiz [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:333:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:368:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:409:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:478:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:505:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:527:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:543:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:919:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:1029:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:1543:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:1840:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:2380:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:2411:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:2478:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:2518:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/hts.h:1551:12: style: Return value '!(*((char*)(&one)))' is always false [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/htslib/hts.h:1551:12: note: Return value '!(*((char*)(&one)))' is always false
htslib-1.21/bcf_sr_sort.c:323:48: style:inconclusive: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent]
htslib-1.21/bcf_sr_sort.h:103:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.21/bcf_sr_sort.c:323:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.21/bcf_sr_sort.c:330:48: style:inconclusive: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent]
htslib-1.21/bcf_sr_sort.h:104:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.21/bcf_sr_sort.c:330:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'.
htslib-1.21/bcf_sr_sort.c:583:85: style:inconclusive: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. [funcArgNamesDifferent]
htslib-1.21/bcf_sr_sort.h:102:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'.
htslib-1.21/bcf_sr_sort.c:583:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'.
htslib-1.21/bcf_sr_sort.c:42:46: style: Parameter 'bs1' can be declared as pointer to const [constParameterPointer]
htslib-1.21/bcf_sr_sort.c:42:62: style: Parameter 'bs2' can be declared as pointer to const [constParameterPointer]
htslib-1.21/bcf_sr_sort.c:223:10: style: Variable 'jmat' can be declared as pointer to const [constVariablePointer]
htslib-1.21/bcf_sr_sort.c:428:24: style: Variable 'var' can be declared as pointer to const [constVariablePointer]
htslib-1.21/bcf_sr_sort.c:540:19: style: Variable 'vset' can be declared as pointer to const [constVariablePointer]
htslib-1.21/htslib/khash_str2int.h:68:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer]
htslib-1.21/htslib/khash_str2int.h:131:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer]
htslib-1.21/htslib/kstring.h:180:39: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.21/htslib/kstring.h:196:40: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.21/annot-tsv.c:309:19: style: Local variable 'tmp' shadows outer variable [shadowVariable]
htslib-1.21/annot-tsv.c:295:11: note: Shadowed declaration
htslib-1.21/annot-tsv.c:309:19: note: Shadow variable
htslib-1.21/annot-tsv.c:432:40: style: Parameter 'dat' can be declared as pointer to const [constParameterPointer]
htslib-1.21/annot-tsv.c:668:53: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
htslib-1.21/annot-tsv.c:761:23: style: Variable 'dst' can be declared as pointer to const [constVariablePointer]
htslib-1.21/annot-tsv.c:762:23: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
htslib-1.21/annot-tsv.c:821:17: style: Variable 'ann' can be declared as pointer to const [constVariablePointer]
htslib-1.21/annot-tsv.c:923:26: style: Variable 'loptions' can be declared as const array [constVariable]
htslib-1.21/textutils_internal.h:361:19: style: Variable 'D' can be declared as const array [constVariable]
htslib-1.21/bgzf.c:1905:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/bgzf.c:2568:27: style: Expression is always true because 'else if' condition is opposite to previous condition at line 2567. [multiCondition]
htslib-1.21/bgzf.c:2567:22: note: first condition
htslib-1.21/bgzf.c:2568:27: note: else if condition is opposite to first condition
htslib-1.21/bgzf.c:330:9: style: Condition '!ed_is_big()' is always true [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/bgzf.c:330:19: note: Calling function 'ed_is_big' returns 0
htslib-1.21/bgzf.c:330:9: note: Condition '!ed_is_big()' is always true
htslib-1.21/bgzf.c:2356:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/bgzf.c:2356:18: note: Calling function 'ed_is_big' returns 0
htslib-1.21/bgzf.c:2356:18: note: Condition 'ed_is_big()' is always false
htslib-1.21/bgzf.c:2452:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/bgzf.c:2452:18: note: Calling function 'ed_is_big' returns 0
htslib-1.21/bgzf.c:2452:18: note: Condition 'ed_is_big()' is always false
htslib-1.21/bgzip.c:55:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzip.c:63:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzip.c:70:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzip.c:105:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzip.c:156:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tv_sec [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzip.c:176:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzip.c:255:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/bgzf.c:1235:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero]
htslib-1.21/bgzf.c:533:25: style:inconclusive: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.21/htslib/bgzf.h:125:36: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/bgzf.c:533:25: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/bgzf.c:610:25: style:inconclusive: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. [funcArgNamesDifferent]
htslib-1.21/htslib/bgzf.h:392:29: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'.
htslib-1.21/bgzf.c:610:25: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'.
htslib-1.21/bgzf.c:2119:40: style:inconclusive: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. [funcArgNamesDifferent]
htslib-1.21/htslib/bgzf.h:322:44: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'.
htslib-1.21/bgzf.c:2119:40: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'.
htslib-1.21/bgzf.c:2226:46: style:inconclusive: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. [funcArgNamesDifferent]
htslib-1.21/htslib/bgzf.h:275:50: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'.
htslib-1.21/bgzf.c:2226:46: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'.
htslib-1.21/bgzf.c:1165:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.21/bgzf.c:1146:13: note: Shadowed declaration
htslib-1.21/bgzf.c:1165:17: note: Shadow variable
htslib-1.21/bgzf.c:1239:18: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer]
htslib-1.21/bgzf.c:2594:24: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/bgzf.c:2600:39: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/htslib/hfile.h:134:33: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/htslib/hfile.h:155:34: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/bgzip.c:159:9: style: Obsolescent function 'utimes' called. It is recommended to use 'utimensat' instead. [prohibitedutimesCalled]
htslib-1.21/bgzip.c:556:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.21/bgzip.c:226:51: note: Shadowed declaration
htslib-1.21/bgzip.c:556:17: note: Shadow variable
htslib-1.21/bgzip.c:170:11: style: Variable 'ext' can be declared as pointer to const [constVariablePointer]
htslib-1.21/htslib/sam.h:1628:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/htslib/sam.h:1699:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:753:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:801:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:965:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:995:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:1456:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:1641:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:1734:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:1810:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:2187:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:2781:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:2820:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_decode.c:175:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_decode.c:2340:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_decode.c:2972:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam_internal.h:57:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_encode.c:1258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_encode.c:3276:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_encode.c:4166:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_codecs.c:2952:62: style: Condition 'option==E_BYTE' is always false [knownConditionTrueFalse]
htslib-1.21/cram/cram_codecs.c:2983:17: style: Condition 'sym>=-1' is always true [knownConditionTrueFalse]
htslib-1.21/cram/cram_codecs.c:2982:19: note: Assignment 'sym=*syms++', assigned value is greater than -1
htslib-1.21/cram/cram_codecs.c:2983:17: note: Condition 'sym>=-1' is always true
htslib-1.21/cram/cram_codecs.c:3108:33: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
htslib-1.21/cram/cram_codecs.c:3107:23: note: Assuming allocation function fails
htslib-1.21/cram/cram_codecs.c:3107:23: note: Assignment 'tmp=malloc(6*c->u.e_huffman.nvals+16)', assigned value is 0
htslib-1.21/cram/cram_codecs.c:3108:33: note: Null pointer addition
htslib-1.21/cram/cram_codecs.c:2119:5: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
htslib-1.21/cram/cram_codecs.c:3196:17: style: Local variable 'k' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_codecs.c:3165:44: note: Shadowed declaration
htslib-1.21/cram/cram_codecs.c:3196:17: note: Shadow variable
htslib-1.21/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-1.21/cram/cram_codecs.c:4019:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:390:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:393:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4021:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:410:70: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:413:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:504:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:439:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:440:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:505:20: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:450:68: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4022:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:548:37: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4014:20: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:562:68: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:793:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:737:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:738:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:794:20: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:748:66: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:813:15: style: Variable 'i32' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:820:14: style: Variable 'i32' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:827:15: style: Variable 'i64' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:834:14: style: Variable 'i64' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4031:20: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:845:66: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:3885:5: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:869:49: note: Parameter 'st' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:982:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:924:60: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:984:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:934:59: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:986:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:945:60: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:960:40: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:988:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:960:59: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1003:35: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1003:54: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1043:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1004:29: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4008:20: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1008:65: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:3887:5: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1031:48: note: Parameter 'st' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4090:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1055:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4088:26: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1073:92: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4092:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1091:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4087:20: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1167:34: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:1192:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:1204:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:1216:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4103:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1327:94: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4105:30: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1342:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4107:30: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1391:94: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4102:19: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1521:35: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:1566:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:1577:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4108:24: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1587:34: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1667:41: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1667:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1667:75: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1667:85: note: Parameter 'out' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1778:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1667:95: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1780:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1671:94: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:1688:55: style: Parameter 'slice' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_codecs.c:1688:74: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1692:41: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1692:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1692:75: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1692:85: note: Parameter 'out' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1782:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1692:95: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:1785:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1703:47: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:1873:19: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:1886:18: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:2023:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1914:35: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1949:41: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1949:60: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2018:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1950:34: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1954:40: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1954:59: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2020:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:1955:33: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:1977:19: style: Variable 'in16' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2046:39: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2046:58: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2046:73: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2046:83: note: Parameter 'out' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2181:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2046:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2051:38: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2051:57: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2051:72: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2051:82: note: Parameter 'out' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2183:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2051:92: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2185:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2108:93: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2409:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2286:35: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2341:39: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2341:58: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2404:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2342:34: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2347:38: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2347:57: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2406:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2348:33: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2507:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2434:90: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2582:17: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2528:89: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2623:42: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2623:61: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2624:42: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2624:52: note: Parameter 'out' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:2870:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2624:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4063:26: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2629:63: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4065:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2643:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4067:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2678:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4069:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2691:61: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4071:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2728:63: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4073:31: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2741:62: note: Parameter 'out_size' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2971:43: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2971:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4064:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:2972:37: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:2979:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3007:42: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3007:61: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4068:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3008:36: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:3015:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3044:43: note: Parameter 'slice' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3044:62: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3045:37: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:3052:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4053:20: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3094:67: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4124:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3484:44: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:3673:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3563:76: note: Parameter 'c' can be declared as pointer to const
htslib-1.21/cram/cram_codecs.c:3566:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:3604:25: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_codecs.c:3623:24: style: Variable 'cp_start' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/cram/cram_codecs.c:4145:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3704:39: note: Parameter 'in' can be declared as pointer to const
htslib-1.21/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-1.21/cram/cram_codecs.c:4144:21: note: You might need to cast the function pointer here
htslib-1.21/cram/cram_codecs.c:3720:45: note: Parameter 'prefix' can be declared as pointer to const
htslib-1.21/cram/cram_io.h:640:49: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_codecs.h:230:52: style: Parameter 'blk' can be declared as pointer to const [constParameterPointer]
htslib-1.21/htslib/sam.h:966:50: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_codecs.c:1661:60: error: Shifting signed 32-bit value by 31 bits is undefined behaviour [shiftTooManyBitsSigned]
htslib-1.21/cram/cram_structs.h:67:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.21/cram/cram_encode.c:828:11: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.21/cram/cram_encode.c:818:11: note: First condition
htslib-1.21/cram/cram_encode.c:828:11: note: Second condition
htslib-1.21/cram/cram_encode.c:3244:27: 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-1.21/cram/cram_encode.c:3245:28: note: Assignment 'c->ref_seq_id=s->hdr->ref_seq_id'
htslib-1.21/cram/cram_encode.c:3244:27: note: Condition 'c->ref_seq_id!=s->hdr->ref_seq_id' is redundant
htslib-1.21/cram/cram_encode.c:4117:25: style: Condition 'c->refs_used' is always true [knownConditionTrueFalse]
htslib-1.21/cram/cram_encode.c:1681:25: style: The comparison 'ret < 0' is always false. [knownConditionTrueFalse]
htslib-1.21/cram/cram_encode.c:1646:15: note: 'ret' is assigned value '0' here.
htslib-1.21/cram/cram_encode.c:1681:25: note: The comparison 'ret < 0' is always false.
htslib-1.21/cram/cram_encode.c:851:13: style: Variable 'methodF' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.21/cram/cram_encode.c:843:17: note: methodF is assigned
htslib-1.21/cram/cram_encode.c:851:13: note: methodF is overwritten
htslib-1.21/cram/cram_encode.c:125:13: style: Local variable 'r' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:88:16: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:125:13: note: Shadow variable
htslib-1.21/cram/cram_encode.c:659:22: style: Local variable 'i32' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:579:13: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:659:22: note: Shadow variable
htslib-1.21/cram/cram_encode.c:955:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:804:28: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:955:13: note: Shadow variable
htslib-1.21/cram/cram_encode.c:973:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:804:28: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:973:13: note: Shadow variable
htslib-1.21/cram/cram_encode.c:1649:13: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:1646:9: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:1649:13: note: Shadow variable
htslib-1.21/cram/cram_encode.c:2862:13: style: Local variable 'key' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:2765:11: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:2862:13: note: Shadow variable
htslib-1.21/cram/cram_encode.c:2899:25: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.21/cram/cram_encode.c:2754:55: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:2899:25: note: Shadow variable
htslib-1.21/cram/cram_encode.c:3717:24: style: Local variable 'brg' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:3707:20: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:3717:24: note: Shadow variable
htslib-1.21/cram/cram_encode.c:3748:25: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_encode.c:3355:9: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:3748:25: note: Shadow variable
htslib-1.21/cram/cram_encode.c:3750:39: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.21/cram/cram_encode.c:3351:58: note: Shadowed declaration
htslib-1.21/cram/cram_encode.c:3750:39: note: Shadow variable
htslib-1.21/cram/cram_encode.c:70:26: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:573:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:803:61: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:1246:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:1304:14: style: Variable 'TC' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:1340:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:1401:20: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:1433:36: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:1477:29: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:1477:58: style: Parameter 'skip' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:1550:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:1657:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:1661:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:1674:28: style: Variable 'L16' can be declared as const array [constVariable]
htslib-1.21/cram/cram_encode.c:1790:21: style: Variable 'm5tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:1795:11: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:1873:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:2544:59: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:2599:51: style: Parameter 'base' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:2653:54: style: Parameter 'base' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_encode.c:3483:27: style: Variable 'sp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:3484:27: style: Variable 'rp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:3485:27: style: Variable 'qp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:3707:20: style: Variable 'brg' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:3717:24: style: Variable 'brg' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:3741:19: style: Variable 'from' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_encode.c:3776:19: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam_internal.h:72:49: style: Parameter 'nib' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:619:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RANS_ORDER_X32 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_decode.c:2306:19: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.21/cram/cram_decode.c:2305:19: note: First condition
htslib-1.21/cram/cram_decode.c:2306:19: note: Second condition
htslib-1.21/cram/cram_decode.c:1512:29: style: Variable 'md_dist' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.21/cram/cram_decode.c:1499:37: note: md_dist is assigned
htslib-1.21/cram/cram_decode.c:1512:29: note: md_dist is overwritten
htslib-1.21/cram/cram_decode.c:2275:34: style:inconclusive: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. [funcArgNamesDifferent]
htslib-1.21/cram/cram_decode.h:114:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'.
htslib-1.21/cram/cram_decode.c:2275:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'.
htslib-1.21/cram/cram_decode.c:881:21: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.21/cram/cram_decode.c:875:72: note: Shadowed declaration
htslib-1.21/cram/cram_decode.c:881:21: note: Shadow variable
htslib-1.21/cram/cram_decode.c:1505:38: style: Local variable 'r' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_decode.c:1099:26: note: Shadowed declaration
htslib-1.21/cram/cram_decode.c:1505:38: note: Shadow variable
htslib-1.21/cram/cram_decode.c:1916:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_decode.c:1903:19: note: Shadowed declaration
htslib-1.21/cram/cram_decode.c:1916:21: note: Shadow variable
htslib-1.21/cram/cram_decode.c:1985:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_decode.c:1957:19: note: Shadowed declaration
htslib-1.21/cram/cram_decode.c:1985:21: note: Shadow variable
htslib-1.21/cram/cram_decode.c:2869:31: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.21/cram/cram_decode.c:2274:52: note: Shadowed declaration
htslib-1.21/cram/cram_decode.c:2869:31: note: Shadow variable
htslib-1.21/cram/cram_decode.c:552:41: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_decode.c:875:55: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_decode.c:926:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:938:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:1229:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:1708:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:1713:35: style: Variable 'refp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:1814:28: style: Variable 'orig_aux_p' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:1888:58: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_decode.c:2233:39: style: Parameter 'md5' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_decode.c:2250:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_decode.c:2286:18: style: Variable 'bfd' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:2435:25: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:3007:41: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_decode.c:3013:11: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_decode.c:3013:17: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/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-1.21/cram/cram_decode.c:1419:34: style: Variable 'dlen' is assigned a value that is never used. [unreadVariable]
htslib-1.21/cram/cram_index.c:670:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_index.c:708:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_index.c:745:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_index.c:836:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId32 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:1512:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:1805:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fqz_slice [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:2479:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:2512:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:2689:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:2850:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:2968:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:3882:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:4315:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:4862:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:4988:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:5720:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:6013:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_external.c:976:8: style: Redundant initialization for 'op'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.21/cram/cram_external.c:967:14: note: op is initialized
htslib-1.21/cram/cram_external.c:976:8: note: op is overwritten
htslib-1.21/cram/cram_external.c:619:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:620:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:621:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:622:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:623:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:624:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:632:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:633:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:634:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:635:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:636:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/cram/cram_external.c:58:40: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:61:34: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:64:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:65:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:67:32: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:75:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:84:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:92:56: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:96:54: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:104:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:120:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:124:48: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:500:61: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:504:59: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:508:54: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:525:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:526:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:527:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:528:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:529:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:530:58: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:533:64: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:554:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:568:50: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:725:61: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_external.c:803:21: style: Variable 'cd' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_external.c:936:49: style: Parameter 'out_rg' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_index.c:478:30: style: Condition 'from->e[k].start<pos' is always true [knownConditionTrueFalse]
htslib-1.21/cram/cram_index.c:473:30: note: Assuming that condition 'from->e[k].start>=pos' is not redundant
htslib-1.21/cram/cram_index.c:478:30: note: Condition 'from->e[k].start<pos' is always true
htslib-1.21/cram/cram_index.c:405:42: style:inconclusive: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. [funcArgNamesDifferent]
htslib-1.21/cram/cram_index.h:54:81: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'.
htslib-1.21/cram/cram_index.c:405:42: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'.
htslib-1.21/cram/cram_index.c:950:54: style:inconclusive: Function 'cram_container_num2offset' argument 2 names different: declaration 'n' definition 'num'. [funcArgNamesDifferent]
htslib-1.21/htslib/cram.h:811:54: note: Function 'cram_container_num2offset' argument 2 names different: declaration 'n' definition 'num'.
htslib-1.21/cram/cram_index.c:950:54: note: Function 'cram_container_num2offset' argument 2 names different: declaration 'n' definition 'num'.
htslib-1.21/cram/cram_index.c:572:50: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_index.c:574:17: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_index.c:999:17: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_index.c:1025:17: style: Variable 'ci' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_index.c:573:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
htslib-1.21/cram/cram_stats.c:95:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/mFILE.c:157:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/mFILE.c:182:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/mFILE.c:198:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/mFILE.c:463:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/mFILE.c:520:13: style: Condition 'len!=size*nmemb' is always true [knownConditionTrueFalse]
htslib-1.21/cram/mFILE.c:511:9: note: len is assigned 'size*nmemb<=mf->size-mf->offset?size*nmemb:mf->size-mf->offset' here.
htslib-1.21/cram/mFILE.c:514:9: note: Assuming condition is false
htslib-1.21/cram/mFILE.c:520:13: note: Condition 'len!=size*nmemb' is always true
htslib-1.21/cram/mFILE.c:264:47: style:inconclusive: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. [funcArgNamesDifferent]
htslib-1.21/cram/mFILE.h:64:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'.
htslib-1.21/cram/mFILE.c:264:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'.
htslib-1.21/cram/mFILE.c:471:20: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/mFILE.c:494:18: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/mFILE.c:527:22: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/open_trace_file.c:195:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/open_trace_file.c:131:31: style: Condition 'i>0' is always true [knownConditionTrueFalse]
htslib-1.21/cram/open_trace_file.c:131:20: note: Assuming that condition 'i==0' is not redundant
htslib-1.21/cram/open_trace_file.c:131:31: note: Condition 'i>0' is always true
htslib-1.21/cram/open_trace_file.c:203:38: style: Checking if unsigned expression 'mfwrite(buf,len,1,mf)' is less than zero. [unsignedLessThanZero]
htslib-1.21/cram/open_trace_file.c:229:50: style: Parameter 'dirname' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/open_trace_file.c:232:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/open_trace_file.c:330:48: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/open_trace_file.c:330:60: style: Parameter 'relative_to' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/string_alloc.c:121:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero]
htslib-1.21/cram/cram_stats.c:168:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/cram/cram_stats.c:135:16: note: Shadowed declaration
htslib-1.21/cram/cram_stats.c:168:13: note: Shadow variable
htslib-1.21/errmod.c:93:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
htslib-1.21/faidx.c:106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.21/faidx.c:365:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.21/faidx.c:408:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SCNu64 [valueFlowBailoutIncompleteVar]
htslib-1.21/faidx.c:473:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/faidx.c:610:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/faidx.c:722:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/errmod.c:34:1: style: Parameter 'array' can be declared as const array [constParameter]
htslib-1.21/faidx.c:241:31: style: Condition 'c!='\n'' is always true [knownConditionTrueFalse]
htslib-1.21/faidx.c:239:27: note: Assuming that condition 'c=='+'' is not redundant
htslib-1.21/faidx.c:241:31: note: Condition 'c!='\n'' is always true
htslib-1.21/htslib/khash.h:449:10: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
htslib-1.21/faidx.c:100:28: note: Assuming allocation function fails
htslib-1.21/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0
htslib-1.21/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0
htslib-1.21/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
htslib-1.21/htslib/khash.h:449:10: note: Null pointer dereference
htslib-1.21/htslib/khash.h:449:38: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
htslib-1.21/faidx.c:100:28: note: Assuming allocation function fails
htslib-1.21/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0
htslib-1.21/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0
htslib-1.21/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
htslib-1.21/htslib/khash.h:449:38: note: Null pointer dereference
htslib-1.21/faidx.c:142:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
htslib-1.21/faidx.c:141:27: note: Assuming allocation function fails
htslib-1.21/faidx.c:141:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0
htslib-1.21/faidx.c:142:5: note: Null pointer dereference
htslib-1.21/faidx.c:143:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
htslib-1.21/faidx.c:141:27: note: Assuming allocation function fails
htslib-1.21/faidx.c:141:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0
htslib-1.21/faidx.c:143:5: note: Null pointer dereference
htslib-1.21/htslib/khash.h:449:13: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
htslib-1.21/faidx.c:100:28: note: Assuming allocation function fails
htslib-1.21/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0
htslib-1.21/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0
htslib-1.21/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
htslib-1.21/htslib/khash.h:449:13: note: Null pointer addition
htslib-1.21/faidx.c:728:24: style: Checking if unsigned expression 'val->line_blen' is less than zero. [unsignedLessThanZero]
htslib-1.21/faidx.c:834:59: style:inconclusive: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.21/htslib/faidx.h:201:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:834:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:846:51: style:inconclusive: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.21/htslib/faidx.h:192:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:846:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:859:49: style:inconclusive: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.21/htslib/faidx.h:190:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:859:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:867:55: style:inconclusive: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.21/htslib/faidx.h:217:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:867:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:879:53: style:inconclusive: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
htslib-1.21/htslib/faidx.h:215:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:879:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'.
htslib-1.21/faidx.c:919:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:189:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:735:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:767:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SSIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:1070:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:1101:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:1209:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:1936:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:1967:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:157:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:187:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:230:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:240:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:286:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:320:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:360:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:371:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:382:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:406:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:422:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:443:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:488:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:501:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:543:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:554:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:599:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:618:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:654:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:725:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:753:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:786:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:824:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:870:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:890:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:898:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hopenv_mem [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:926:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:1044:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:1146:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile.c:599:17: style: Condition 'ret<0' is always false [knownConditionTrueFalse]
htslib-1.21/hfile.c:588:15: note: Assignment 'ret=0', assigned value is 0
htslib-1.21/hfile.c:599:17: note: Condition 'ret<0' is always false
htslib-1.21/hfile.c:600:18: style: Condition 'ret<0' is always false [knownConditionTrueFalse]
htslib-1.21/hfile.c:588:15: note: Assignment 'ret=0', assigned value is 0
htslib-1.21/hfile.c:600:18: note: Condition 'ret<0' is always false
htslib-1.21/hfile.c:1037:57: style: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true [knownConditionTrueFalse]
htslib-1.21/hfile.c:1037:39: note: Calling function 'try_exe_add_scheme_handler' returns -1
htslib-1.21/hfile.c:1037:57: note: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true
htslib-1.21/hfile.c:1292:26: style:inconclusive: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent]
htslib-1.21/htslib/hfile.h:74:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.21/hfile.c:1292:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.21/hfile.c:1320:27: style:inconclusive: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent]
htslib-1.21/htslib/hfile.h:99:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.21/hfile.c:1320:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'.
htslib-1.21/hfile.c:1340:46: style:inconclusive: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. [funcArgNamesDifferent]
htslib-1.21/htslib/hfile.h:114:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'.
htslib-1.21/hfile.c:1340:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'.
htslib-1.21/hfile.c:163:50: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile.c:235:11: style: Variable 'found' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile.c:572:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/hfile.c:624:33: note: You might need to cast the function pointer here
htslib-1.21/hfile.c:586:28: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.21/hfile.c:606:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/hfile.c:797:17: note: You might need to cast the function pointer here
htslib-1.21/hfile.c:784:30: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.21/hfile.c:790:29: style: Parameter 'fpv' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile.c:868:35: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile.c:1378:9: style: struct member 'knetFile_s::type' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1380:11: style: struct member 'knetFile_s::host' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1380:18: style: struct member 'knetFile_s::port' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1381:9: style: struct member 'knetFile_s::ctrl_fd' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1381:18: style: struct member 'knetFile_s::pasv_ip' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1381:30: style: struct member 'knetFile_s::pasv_port' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1381:41: style: struct member 'knetFile_s::max_response' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1381:55: style: struct member 'knetFile_s::no_reconnect' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1381:69: style: struct member 'knetFile_s::is_ready' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1382:11: style: struct member 'knetFile_s::response' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1382:22: style: struct member 'knetFile_s::retr' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1382:29: style: struct member 'knetFile_s::size_cmd' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1383:13: style: struct member 'knetFile_s::seek_offset' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1384:13: style: struct member 'knetFile_s::file_size' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1385:11: style: struct member 'knetFile_s::path' is never used. [unusedStructMember]
htslib-1.21/hfile.c:1385:18: style: struct member 'knetFile_s::http_host' is never used. [unusedStructMember]
htslib-1.21/cram/cram_io.c:4323:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/hfile_gcs.c:75:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_gcs.c:145:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gcs_vopen [valueFlowBailoutIncompleteVar]
htslib-1.21/cram/cram_io.c:2402:11: warning: Either the condition '!r' is redundant or there is possible null pointer dereference: r. [nullPointerRedundantCheck]
htslib-1.21/cram/cram_io.c:2405:9: note: Assuming that condition '!r' is not redundant
htslib-1.21/cram/cram_io.c:2402:11: note: Null pointer dereference
htslib-1.21/cram/cram_io.c:5245:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.21/cram/cram_io.c:5244:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
htslib-1.21/cram/cram_io.c:5245:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
htslib-1.21/cram/cram_io.c:5246:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.21/cram/cram_io.c:5245:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
htslib-1.21/cram/cram_io.c:5246:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
htslib-1.21/cram/cram_io.c:5247:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
htslib-1.21/cram/cram_io.c:5246:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
htslib-1.21/cram/cram_io.c:5247:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
htslib-1.21/cram/cram_io.c:4914:61: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/cram/cram_io.c:4983:93: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/cram/cram_io.c:4990:95: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/cram/cram_io.c:137:39: style:inconclusive: Function 'itf8_decode' argument 2 names different: declaration 'val' definition 'val_p'. [funcArgNamesDifferent]
htslib-1.21/cram/cram_io.h:69:39: note: Function 'itf8_decode' argument 2 names different: declaration 'val' definition 'val_p'.
htslib-1.21/cram/cram_io.c:137:39: note: Function 'itf8_decode' argument 2 names different: declaration 'val' definition 'val_p'.
htslib-1.21/cram/cram_io.c:4030:55: style:inconclusive: Function 'cram_write_container' argument 2 names different: declaration 'h' definition 'c'. [funcArgNamesDifferent]
htslib-1.21/htslib/cram.h:570:55: note: Function 'cram_write_container' argument 2 names different: declaration 'h' definition 'c'.
htslib-1.21/cram/cram_io.c:4030:55: note: Function 'cram_write_container' argument 2 names different: declaration 'h' definition 'c'.
htslib-1.21/cram/cram_io.c:3762:29: style: Local variable 'c' shadows outer argument [shadowArgument]
htslib-1.21/cram/cram_io.c:3712:42: note: Shadowed declaration
htslib-1.21/cram/cram_io.c:3762:29: note: Shadow variable
htslib-1.21/cram/cram_io.c:138:16: style: Variable 'nbytes' can be declared as const array [constVariable]
htslib-1.21/cram/cram_io.c:146:16: style: Variable 'nbits' can be declared as const array [constVariable]
htslib-1.21/cram/cram_io.c:196:16: style: Variable 'nbytes' can be declared as const array [constVariable]
htslib-1.21/cram/cram_io.c:204:16: style: Variable 'nbits' can be declared as const array [constVariable]
htslib-1.21/cram/cram_io.c:1928:9: style: Variable 'methmap' can be declared as const array [constVariable]
htslib-1.21/cram/cram_io.c:2116:24: style: Variable 'meth_cost' can be declared as const array [constVariable]
htslib-1.21/cram/cram_io.c:2475:44: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_io.c:2769:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_io.c:2829:45: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_io.c:2847:48: style: Parameter 'dir' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_io.c:2848:16: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_io.c:3273:15: style: Variable 'cp_to' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_io.c:3514:28: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_io.c:3954:41: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_io.c:4859:40: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_io.c:4928:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_io.c:5296:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/cram/cram_io.c:5686:23: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
htslib-1.21/cram/cram_io.c:5826:21: style: Variable 'r' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_gcs.c:104:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/hfile_gcs.c:105:24: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/hfile_gcs.c:112:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/cram/cram_io.c:2283:15: style: Variable 'strat' is assigned a value that is never used. [unreadVariable]
htslib-1.21/cram/cram_io.c:3515:25: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
htslib-1.21/hfile_s3.c:127:0: error: #error No HMAC() routine found by configure [preprocessorErrorDirective]
htslib-1.21/hfile_s3.c:127:2: error: #error No HMAC() routine found by configure [preprocessorErrorDirective]
htslib-1.21/hfile_libcurl.c:131:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOSYS [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:160:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:240:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EBADF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:282:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:315:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:329:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:370:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:513:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:568:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:701:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLM_OK [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:750:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_WRITEFUNC_PAUSE [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:767:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:826:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:870:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_READFUNC_PAUSE [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:889:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:934:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:1016:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:1134:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:1188:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:1436:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_libcurl.c:1505:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vhopen_libcurl [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:157:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:170:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:216:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:256:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_CUSTOMREQUEST [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:322:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_POST [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:404:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_UPLOAD [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:440:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:506:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLINFO_RESPONSE_CODE [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:572:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:613:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_URL [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:649:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:682:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:779:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:804:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:826:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:839:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vhopen_s3_write [valueFlowBailoutIncompleteVar]
htslib-1.21/hfile_s3_write.c:165:38: style: Parameter 'start_tag' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_s3_write.c:165:55: style: Parameter 'end_tag' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_s3_write.c:167:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_s3_write.c:286:59: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_s3_write.c:371:55: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_s3_write.c:584:61: style: Parameter 'head' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_s3_write.c:584:78: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_s3_write.c:662:64: style: Parameter 'auth' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_s3_write.c:798:22: style: Variable 'args2' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_libcurl.c:797:23: style: Condition 'bytes<n' is always false [knownConditionTrueFalse]
htslib-1.21/hfile_libcurl.c:795:26: note: bytes is assigned 'n<=nbytes?n:nbytes' here.
htslib-1.21/hfile_libcurl.c:797:23: note: Condition 'bytes<n' is always false
htslib-1.21/hfile_libcurl.c:418:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_libcurl.c:561:15: style: Variable 'header' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/hfile_libcurl.c:1228:66: note: You might need to cast the function pointer here
htslib-1.21/hfile_libcurl.c:743:35: note: Parameter 'ptr' can be declared as pointer to const
htslib-1.21/hfile_libcurl.c:794:19: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_libcurl.c:1014:28: style: Variable 'list' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_libcurl.c:1168:64: style: Parameter 'headers' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hfile_libcurl.c:1171:24: style: Variable 'list' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_libcurl.c:1245:15: style: Variable 'env_curl_ca_bundle' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hfile_libcurl.c:1414:22: style: Variable 'args2' can be declared as pointer to const [constVariablePointer]
htslib-1.21/htslib/hts_expr.h:80:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
htslib-1.21/hts_expr.c:268:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/hts_expr.c:292:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/hts_expr.c:757:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REG_EXTENDED [valueFlowBailoutIncompleteVar]
htslib-1.21/hts_expr.c:885:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/header.c:191:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/header.c:672:43: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/header.c:1104:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/header.c:1335:47: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/header.c:2313:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/header.c:2329:65: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/header.c:1207:34: style:inconclusive: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:445:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1207:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1214:36: style:inconclusive: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:458:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1214:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1221:35: style:inconclusive: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:465:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1221:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1286:34: style:inconclusive: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:483:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1286:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1321:33: style:inconclusive: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:499:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1321:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1354:37: style:inconclusive: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:518:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1354:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1378:38: style:inconclusive: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:536:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1378:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1412:39: style:inconclusive: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:561:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1412:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1451:40: style:inconclusive: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:573:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1451:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1538:36: style:inconclusive: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:600:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1538:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1643:38: style:inconclusive: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:617:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1643:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1699:37: style:inconclusive: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:657:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1699:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1699:81: style:inconclusive: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:657:80: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'.
htslib-1.21/header.c:1699:81: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'.
htslib-1.21/header.c:1771:36: style:inconclusive: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:666:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1771:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1911:36: style:inconclusive: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:707:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1911:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1943:37: style:inconclusive: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:725:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1943:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1974:38: style:inconclusive: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:736:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:1974:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2021:33: style:inconclusive: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:749:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2021:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2190:38: style:inconclusive: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:792:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2190:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2241:31: style:inconclusive: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:810:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2241:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2346:34: style:inconclusive: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:830:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:2346:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/header.c:66:64: style: Parameter 'type_list' can be declared as pointer to const [constParameterPointer]
htslib-1.21/header.c:587:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:587:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:624:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:624:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:733:10: style: Variable 'c' can be declared as const array [constVariable]
htslib-1.21/header.c:1177:22: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1366:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1390:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1500:11: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1502:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1701:15: style: Variable 'rh' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1729:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1745:22: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1931:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:1962:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:2498:27: style: Variable 't2' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:2573:15: style: Variable 'k' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:2573:19: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:2671:25: style: Variable 'sn_tag' can be declared as pointer to const [constVariablePointer]
htslib-1.21/header.c:41:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.21/header.c:1750:17: style: Variable 'head' is assigned a value that is never used. [unreadVariable]
htslib-1.21/htsfile.c:51:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/htsfile.c:72:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/htsfile.c:116:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/htsfile.c:155:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/htsfile.c:257:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/kstring.c:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/kstring.c:277:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/kstring.c:310:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/kstring.c:187:44: style:inconclusive: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'. [funcArgNamesDifferent]
htslib-1.21/htslib/kstring.h:117:45: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
htslib-1.21/kstring.c:187:44: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
htslib-1.21/kstring.c:379:31: style: Variable 'bmBc' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:86:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_VERSION_TEXT [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:152:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_CC [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:965:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:1486:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:1630:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:1980:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2028:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2062:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2123:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2213:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2214:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2492:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2544:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2775:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2827:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2847:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2902:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:2953:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:3015:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:3152:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:3387:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:3758:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:4132:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:4226:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:4290:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:4624:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:4880:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:4966:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:5002:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:5063:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:5139:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/hts_expr.c:104:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.21/hts_expr.c:101:14: note: l is initialized
htslib-1.21/hts_expr.c:104:12: note: l is overwritten
htslib-1.21/hts_expr.c:121:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.21/hts_expr.c:118:14: note: l is initialized
htslib-1.21/hts_expr.c:121:12: note: l is overwritten
htslib-1.21/hts_expr.c:138:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization]
htslib-1.21/hts_expr.c:135:14: note: l is initialized
htslib-1.21/hts_expr.c:138:12: note: l is overwritten
htslib-1.21/hts_expr.c:48:9: style: struct member 'hts_filter_t::parsed' is never used. [unusedStructMember]
htslib-1.21/multipart.c:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/multipart.c:122:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/multipart.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/multipart.c:259:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/md5.c:271:35: style:inconclusive: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:1487:39: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'.
htslib-1.21/md5.c:271:35: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'.
htslib-1.21/multipart.c:89:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/multipart.c:90:68: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/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-1.21/multipart.c:140:21: note: You might need to cast the function pointer here
htslib-1.21/multipart.c:114:39: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.21/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-1.21/multipart.c:140:38: note: You might need to cast the function pointer here
htslib-1.21/multipart.c:120:36: note: Parameter 'fpv' can be declared as pointer to const
htslib-1.21/plugin.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/plugin.c:77:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUGIN_EXT [valueFlowBailoutIncompleteVar]
htslib-1.21/plugin.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/plugin.c:190:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/probaln.c:86:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/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-1.21/plugin.c:107:24: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.21/realn.c:94:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/realn.c:216:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/probaln.c:182:16: style: Variable 'E' can be declared as const array [constVariable]
htslib-1.21/probaln.c:305:16: style: Variable 'E' can be declared as const array [constVariable]
htslib-1.21/probaln.c:381:27: style: Variable 'fi' can be declared as pointer to const [constVariablePointer]
htslib-1.21/probaln.c:381:46: style: Variable 'bi' can be declared as pointer to const [constVariablePointer]
htslib-1.21/probaln.c:416:25: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
htslib-1.21/regidx.c:164:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/realn.c:58:51: style: Condition 'qual[z]>=13' is always true [knownConditionTrueFalse]
htslib-1.21/realn.c:56:53: note: Assuming that condition 'qual[z]>=13' is not redundant
htslib-1.21/realn.c:58:51: note: Condition 'qual[z]>=13' is always true
htslib-1.21/realn.c:41:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/realn.c:42:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/realn.c:43:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
htslib-1.21/realn.c:111:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/realn.c:112:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
htslib-1.21/realn.c:205:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/realn.c:48:27: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
htslib-1.21/realn.c:73:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
htslib-1.21/realn.c:77:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
htslib-1.21/regidx.c:440:68: style: Condition 'list->reg[ireg].beg<=end' is always true [knownConditionTrueFalse]
htslib-1.21/regidx.c:439:38: note: Assuming that condition 'list->reg[ireg].beg>end' is not redundant
htslib-1.21/regidx.c:440:68: note: Condition 'list->reg[ireg].beg<=end' is always true
htslib-1.21/regidx.c:631:63: style: Condition 'list->reg[i].beg<=itr->end' is always true [knownConditionTrueFalse]
htslib-1.21/regidx.c:630:31: note: Assuming that condition 'list->reg[i].beg>itr->end' is not redundant
htslib-1.21/regidx.c:631:63: note: Condition 'list->reg[i].beg<=itr->end' is always true
htslib-1.21/regidx.c:209:42: style:inconclusive: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:150:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
htslib-1.21/regidx.c:209:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
htslib-1.21/regidx.c:209:119: style:inconclusive: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:150:121: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.21/regidx.c:209:119: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.21/regidx.c:246:114: style:inconclusive: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:148:113: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.21/regidx.c:246:114: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
htslib-1.21/regidx.c:401:30: style:inconclusive: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:167:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.21/regidx.c:401:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.21/regidx.c:401:95: style:inconclusive: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:167:92: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:401:95: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:584:33: style:inconclusive: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:212:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.21/regidx.c:584:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.21/regidx.c:599:29: style:inconclusive: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:216:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.21/regidx.c:599:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
htslib-1.21/regidx.c:599:47: style:inconclusive: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:216:44: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:599:47: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:606:31: style:inconclusive: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:214:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:606:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:612:30: style:inconclusive: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:223:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:612:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:646:27: style:inconclusive: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
htslib-1.21/htslib/regidx.h:230:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:646:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
htslib-1.21/regidx.c:105:35: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.21/regidx.c:132:35: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
htslib-1.21/regidx.c:132:45: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
htslib-1.21/regidx.c:151:38: style: Parameter 'chr_beg' can be declared as pointer to const [constParameterPointer]
htslib-1.21/regidx.c:151:53: style: Parameter 'chr_end' can be declared as pointer to const [constParameterPointer]
htslib-1.21/regidx.c:151:98: style: Parameter 'payload' can be declared as pointer to const [constParameterPointer]
htslib-1.21/regidx.c:684:13: style: Variable 'src_itr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/regidx.c:48:15: style: struct member 'pos_t::pos' is never used. [unusedStructMember]
htslib-1.21/regidx.c:49:15: style: struct member 'pos_t::ireg' is never used. [unusedStructMember]
htslib-1.21/region.c:43:21: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
htslib-1.21/region.c:44:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/region.c:87:35: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/sam_mods.c:601:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/sam_mods.c:559:35: note: Shadowed declaration
htslib-1.21/sam_mods.c:601:13: note: Shadow variable
htslib-1.21/sam_mods.c:206:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam_mods.c:248:14: style: Variable 'mi' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam_mods.c:264:14: style: Variable 'ml_end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam_mods.c:482:15: style: Variable 'MMptr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam_mods.c:647:44: style: Parameter 'state' can be declared as pointer to const [constParameterPointer]
htslib-1.21/sam_mods.c:274:18: style: Variable 'implicit' is assigned a value that is never used. [unreadVariable]
htslib-1.21/samples/add_header.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/cram.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/cram.c:53:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/dump_aux.c:126:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/dump_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/sam.c:437:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:555:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:689:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:862:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:943:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:1010:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:1122:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:1893:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:2187:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:2218:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:2353:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:2430:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:2946:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:3347:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EIO [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:3444:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:3599:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:3710:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:3874:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4238:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4275:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4388:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4487:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4512:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4723:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4836:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4880:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4889:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4918:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4925:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4935:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:4953:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5005:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5074:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5109:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5167:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5193:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5202:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5209:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5219:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:5229:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:6122:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:6221:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:6355:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/flags_demo.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/flags_demo.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/flags_htsopt_field.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/flags_htsopt_field.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/index_fasta.c:57:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/index_fasta.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/index_multireg_read.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/index_multireg_read.c:117:12: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
htslib-1.21/samples/index_multireg_read.c:74:9: warning: If memory allocation fails, then there is a possible null pointer dereference: regions [nullPointerOutOfMemory]
htslib-1.21/samples/index_multireg_read.c:70:21: note: Assuming allocation function fails
htslib-1.21/samples/index_multireg_read.c:70:21: note: Assignment 'regions=calloc(regcnt,sizeof(char*))', assigned value is 0
htslib-1.21/samples/index_multireg_read.c:74:9: note: Null pointer dereference
htslib-1.21/samples/index_reg_read.c:68:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/index_write.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/mod_aux.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/mod_aux.c:116:27: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
htslib-1.21/samples/mod_aux_ba.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/mod_aux_ba.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/mod_bam.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/modstate.c:64:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/modstate.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/modstate.c:56:77: style: Variable 'bm' can be declared as pointer to const [constVariablePointer]
htslib-1.21/samples/mpileup.c:96:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/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-1.21/samples/mpileup.c:138:36: note: You might need to cast the function pointer here
htslib-1.21/samples/mpileup.c:56:26: note: Parameter 'data' can be declared as pointer to const
htslib-1.21/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-1.21/samples/mpileup.c:138:36: note: You might need to cast the function pointer here
htslib-1.21/samples/mpileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const
htslib-1.21/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-1.21/samples/mpileup.c:139:35: note: You might need to cast the function pointer here
htslib-1.21/samples/mpileup.c:60:25: note: Parameter 'data' can be declared as pointer to const
htslib-1.21/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-1.21/samples/mpileup.c:139:35: note: You might need to cast the function pointer here
htslib-1.21/samples/mpileup.c:60:63: note: Parameter 'cd' can be declared as pointer to const
htslib-1.21/samples/pileup.c:104:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/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-1.21/samples/pileup.c:131:34: note: You might need to cast the function pointer here
htslib-1.21/samples/pileup.c:56:26: note: Parameter 'data' can be declared as pointer to const
htslib-1.21/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-1.21/samples/pileup.c:131:34: note: You might need to cast the function pointer here
htslib-1.21/samples/pileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const
htslib-1.21/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-1.21/samples/pileup.c:132:33: note: You might need to cast the function pointer here
htslib-1.21/samples/pileup.c:65:25: note: Parameter 'data' can be declared as pointer to const
htslib-1.21/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-1.21/samples/pileup.c:132:33: note: You might need to cast the function pointer here
htslib-1.21/samples/pileup.c:65:63: note: Parameter 'cd' can be declared as pointer to const
htslib-1.21/samples/pileup_mod.c:109:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/qtask_ordered.c:157:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qseq [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/qtask_ordered.c:198:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/qtask_ordered.c:241:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/qtask_ordered.c:164:78: portability:inconclusive: Casting from float * to const unsigned char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
htslib-1.21/samples/qtask_ordered.c:148:14: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
htslib-1.21/samples/qtask_ordered.c:223:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/qtask_ordered.c:145:20: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
htslib-1.21/samples/qtask_ordered.c:147:19: style: Variable 'gcratio' is assigned a value that is never used. [unreadVariable]
htslib-1.21/samples/qtask_ordered.c:156:14: style: Variable 'data' is assigned a value that is never used. [unreadVariable]
htslib-1.21/samples/qtask_ordered.c:181:11: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
htslib-1.21/samples/qtask_unordered.c:157:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qseq [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/qtask_unordered.c:196:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/qtask_unordered.c:153:14: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
htslib-1.21/samples/qtask_unordered.c:181:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/qtask_unordered.c:152:18: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
htslib-1.21/samples/qtask_unordered.c:156:14: style: Variable 'data' is assigned a value that is never used. [unreadVariable]
htslib-1.21/samples/read_aux.c:122:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/read_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/read_bam.c:63:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/read_bam.c:114:18: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/samples/read_bam.c:55:20: note: Shadowed declaration
htslib-1.21/samples/read_bam.c:114:18: note: Shadow variable
htslib-1.21/samples/read_bam.c:48:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/read_fast.c:58:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/read_fast.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/read_fast_index.c:58:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FAI_FASTA [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/read_fast_index.c:53:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/read_header.c:56:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/read_refname.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/read_refname.c:91:13: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
htslib-1.21/samples/read_refname.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/rem_header.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/rem_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/split.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/split.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/split2.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/split2.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/split_thread1.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/split_thread1.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/split_thread2.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/split_thread2.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/update_header.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/update_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/samples/write_fast.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/samples/write_fast.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter]
htslib-1.21/synced_bcf_reader.c:88:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:128:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pair [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:203:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:222:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable targets_overlap [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:423:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:458:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:466:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:523:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:679:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:772:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:870:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:1011:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:1453:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/synced_bcf_reader.c:422:5: warning: If memory allocation fails, then there is a possible null pointer dereference: files [nullPointerOutOfMemory]
htslib-1.21/synced_bcf_reader.c:421:43: note: Assuming allocation function fails
htslib-1.21/synced_bcf_reader.c:421:24: note: Assignment 'files=(struct bcf_srs_t*)calloc(1,sizeof(struct bcf_srs_t))', assigned value is 0
htslib-1.21/synced_bcf_reader.c:422:5: note: Null pointer dereference
htslib-1.21/synced_bcf_reader.c:423:23: warning: If memory allocation fails, then there is a possible null pointer dereference: files [nullPointerOutOfMemory]
htslib-1.21/synced_bcf_reader.c:421:43: note: Assuming allocation function fails
htslib-1.21/synced_bcf_reader.c:421:24: note: Assignment 'files=(struct bcf_srs_t*)calloc(1,sizeof(struct bcf_srs_t))', assigned value is 0
htslib-1.21/synced_bcf_reader.c:423:23: note: Null pointer dereference
htslib-1.21/synced_bcf_reader.c:251:34: style:inconclusive: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:237:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:251:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:445:32: style:inconclusive: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:204:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:445:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:825:33: style:inconclusive: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:251:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:825:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:896:35: style:inconclusive: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:281:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:896:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'.
htslib-1.21/synced_bcf_reader.c:896:54: style:inconclusive: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:281:56: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'.
htslib-1.21/synced_bcf_reader.c:896:54: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'.
htslib-1.21/synced_bcf_reader.c:1203:77: style:inconclusive: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:348:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'.
htslib-1.21/synced_bcf_reader.c:1203:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'.
htslib-1.21/synced_bcf_reader.c:1203:87: style:inconclusive: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:348:86: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'.
htslib-1.21/synced_bcf_reader.c:1203:87: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'.
htslib-1.21/synced_bcf_reader.c:1203:98: style:inconclusive: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:348:96: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'.
htslib-1.21/synced_bcf_reader.c:1203:98: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'.
htslib-1.21/synced_bcf_reader.c:1282:47: style:inconclusive: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:351:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.21/synced_bcf_reader.c:1282:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.21/synced_bcf_reader.c:1307:43: style:inconclusive: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:360:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.21/synced_bcf_reader.c:1307:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'.
htslib-1.21/synced_bcf_reader.c:1307:60: style:inconclusive: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:360:64: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'.
htslib-1.21/synced_bcf_reader.c:1307:60: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'.
htslib-1.21/synced_bcf_reader.c:1514:44: style:inconclusive: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. [funcArgNamesDifferent]
htslib-1.21/htslib/synced_bcf_reader.h:390:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'.
htslib-1.21/synced_bcf_reader.c:1514:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'.
htslib-1.21/synced_bcf_reader.c:1476:33: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/synced_bcf_reader.c:149:37: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/synced_bcf_reader.c:396:20: style: Variable 'hdr0' can be declared as pointer to const [constVariablePointer]
htslib-1.21/synced_bcf_reader.c:397:20: style: Variable 'hdr1' can be declared as pointer to const [constVariablePointer]
htslib-1.21/synced_bcf_reader.c:502:40: style: Parameter 'reader' can be declared as pointer to const [constParameterPointer]
htslib-1.21/synced_bcf_reader.c:502:56: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
htslib-1.21/synced_bcf_reader.c:595:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
htslib-1.21/synced_bcf_reader.c:596:19: style: Variable 'alt' can be declared as pointer to const [constVariablePointer]
htslib-1.21/synced_bcf_reader.c:1021:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
htslib-1.21/synced_bcf_reader.c:1022:16: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
htslib-1.21/synced_bcf_reader.c:1352:20: style: Variable 'creg' can be declared as pointer to const [constVariablePointer]
htslib-1.21/tabix.c:64:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/tabix.c:76:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/tabix.c:117:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/tabix.c:170:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/tabix.c:499:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/tabix.c:657:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/sam.c:3322:21: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/sam.c:3342:21: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/sam.c:3623:33: 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-1.21/sam.c:257:17: style: Condition 'bufsize<h->l_text' is always false [knownConditionTrueFalse]
htslib-1.21/sam.c:256:13: note: bufsize is assigned 'h->l_text+1' here.
htslib-1.21/sam.c:257:17: note: Condition 'bufsize<h->l_text' is always false
htslib-1.21/sam.c:961:17: style: Condition 'new_len<1' is always false [knownConditionTrueFalse]
htslib-1.21/sam.c:960:36: note: Assignment 'new_len=strlen(qname)+1', assigned value is greater than 0
htslib-1.21/sam.c:961:17: note: Condition 'new_len<1' is always false
htslib-1.21/sam.c:5329:50: style: Condition 'strncmp(format,"fa",format_len)==0' is always false [knownConditionTrueFalse]
htslib-1.21/sam.c:6088:39: style: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true [knownConditionTrueFalse]
htslib-1.21/sam.c:6088:39: note: Calling function 'resolve_cigar2' returns 1
htslib-1.21/sam.c:6088:39: note: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true
htslib-1.21/sam.c:4512:15: warning: Either the condition 'x' is redundant or there is possible null pointer dereference: x. [nullPointerRedundantCheck]
htslib-1.21/sam.c:4516:9: note: Assuming that condition 'x' is not redundant
htslib-1.21/sam.c:4512:15: note: Null pointer dereference
htslib-1.21/sam.c:5724:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
htslib-1.21/sam.c:5724:5: note: Null pointer dereference
htslib-1.21/sam.c:5725:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
htslib-1.21/sam.c:5725:5: note: Null pointer dereference
htslib-1.21/sam.c:5725:18: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
htslib-1.21/sam.c:5725:18: note: Null pointer dereference
htslib-1.21/sam.c:5725:40: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
htslib-1.21/sam.c:5725:40: note: Null pointer dereference
htslib-1.21/sam.c:5726:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
htslib-1.21/sam.c:5726:5: note: Null pointer dereference
htslib-1.21/sam.c:5726:21: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
htslib-1.21/sam.c:5726:21: note: Null pointer dereference
htslib-1.21/sam.c:5727:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
htslib-1.21/sam.c:5727:5: note: Null pointer dereference
htslib-1.21/sam.c:6266:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6266:5: note: Null pointer dereference
htslib-1.21/sam.c:6267:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6267:5: note: Null pointer dereference
htslib-1.21/sam.c:6268:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6268:5: note: Null pointer dereference
htslib-1.21/sam.c:6269:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6269:5: note: Null pointer dereference
htslib-1.21/sam.c:6270:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6270:5: note: Null pointer dereference
htslib-1.21/sam.c:6271:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6271:5: note: Null pointer dereference
htslib-1.21/sam.c:6272:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6272:5: note: Null pointer dereference
htslib-1.21/sam.c:6273:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6273:5: note: Null pointer dereference
htslib-1.21/sam.c:6275:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6275:9: note: Null pointer dereference
htslib-1.21/sam.c:6276:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6276:9: note: Null pointer dereference
htslib-1.21/sam.c:6276:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6276:24: note: Null pointer dereference
htslib-1.21/sam.c:6277:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6277:9: note: Null pointer dereference
htslib-1.21/sam.c:6277:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
htslib-1.21/sam.c:6277:24: note: Null pointer dereference
htslib-1.21/sam.c:5871:29: style: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value. [duplicateExpression]
htslib-1.21/sam.c:5869:31: note: 'iref' is assigned value 'b->core.pos' here.
htslib-1.21/sam.c:5871:29: note: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value.
htslib-1.21/sam.c:2404:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/sam.c:116:33: style:inconclusive: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:385:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/sam.c:116:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'.
htslib-1.21/sam.c:954:27: style:inconclusive: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. [funcArgNamesDifferent]
htslib-1.21/htslib/sam.h:1115:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'.
htslib-1.21/sam.c:954:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'.
htslib-1.21/sam.c:2091:25: style: Local variable 'absent' shadows outer variable [shadowVariable]
htslib-1.21/sam.c:2056:20: note: Shadowed declaration
htslib-1.21/sam.c:2091:25: note: Shadow variable
htslib-1.21/sam.c:2836:19: style: Local variable 'end' shadows outer argument [shadowArgument]
htslib-1.21/sam.c:2730:48: note: Shadowed declaration
htslib-1.21/sam.c:2836:19: note: Shadow variable
htslib-1.21/sam.c:3013:43: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/sam.c:2913:9: note: Shadowed declaration
htslib-1.21/sam.c:3013:43: note: Shadow variable
htslib-1.21/sam.c:4273:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
htslib-1.21/sam.c:4259:9: note: Shadowed declaration
htslib-1.21/sam.c:4273:17: note: Shadow variable
htslib-1.21/sam.c:4448:18: style: Local variable 's' shadows outer variable [shadowVariable]
htslib-1.21/sam.c:4417:14: note: Shadowed declaration
htslib-1.21/sam.c:4448:18: note: Shadow variable
htslib-1.21/sam.c:5635:25: style: Local variable 'j' shadows outer variable [shadowVariable]
htslib-1.21/sam.c:5575:9: note: Shadowed declaration
htslib-1.21/sam.c:5635:25: note: Shadow variable
htslib-1.21/sam.c:346:11: style: Variable 'text' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:395:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:688:14: style: Variable 'CG' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:1206:14: style: Variable 'hb' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:1216:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:1306:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:1434:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:1609:17: style: Variable 's' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:1634:11: style: Variable 'fd' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:2061:19: style: Variable 'tab' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:2247:15: style: Variable 'text' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:2321:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:2331:18: style: Variable 'tmp' can be declared as const array [constVariable]
htslib-1.21/sam.c:2658:15: style: Variable 'r' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:2731:43: style: Parameter 'tag_whitelist' can be declared as pointer to const [constParameterPointer]
htslib-1.21/sam.c:2735:23: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:2912:22: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:2963:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:3518:34: 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-1.21/sam.c:3654:42: note: You might need to cast the function pointer here
htslib-1.21/sam.c:3518:34: note: Parameter 'arg' can be declared as pointer to const
htslib-1.21/sam.c:3607:19: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:3608:19: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:3861:14: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4055:15: style: Variable 'bc' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4103:11: style: Variable 'name' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4233:57: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/sam.c:4377:26: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4417:14: style: Variable 's' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4417:18: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4432:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4743:22: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4879:14: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4905:22: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:4955:39: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:5102:62: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
htslib-1.21/sam.c:5271:11: style: Variable 'opts' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:5470:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:5471:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:5576:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:5867:14: style: Variable 'a_seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:5867:40: style: Variable 'b_seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/sam.c:1099:32: 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-1.21/sam.c:61:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.21/tabix.c:206:52: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer]
htslib-1.21/tabix.c:437:81: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer]
htslib-1.21/tabix.c:460:15: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer]
htslib-1.21/tabix.c:618:11: style: Variable 'reheader' can be declared as pointer to const [constVariablePointer]
htslib-1.21/tabix.c:784:11: style: Variable 'suffix' can be declared as pointer to const [constVariablePointer]
htslib-1.21/tbx.c:185:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/tbx.c:472:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/fieldarith.c:42:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/fieldarith.c:37:14: style: Variable 'aux' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/fuzz/hts_open_fuzzer.c:46:62: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/fuzz/hts_open_fuzzer.c:121:62: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer]
htslib-1.21/tbx.c:281:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/tbx.c:281:18: note: Calling function 'ed_is_big' returns 0
htslib-1.21/tbx.c:281:18: note: Condition 'ed_is_big()' is always false
htslib-1.21/test/hfile.c:41:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/hfile.c:57:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/hfile.c:108:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/tbx.c:286:13: style: Local variable 'x' shadows outer variable [shadowVariable]
htslib-1.21/tbx.c:264:14: note: Shadowed declaration
htslib-1.21/tbx.c:286:13: note: Shadow variable
htslib-1.21/tbx.c:443:11: style: Variable 'nm' can be declared as pointer to const [constVariablePointer]
htslib-1.21/tbx.c:111:36: style: Variable 'nodeid' is assigned a value that is never used. [unreadVariable]
htslib-1.21/hts.c:1293:21: style: Redundant condition: The condition '*str' is redundant since '*str == ','' is sufficient. [redundantCondition]
htslib-1.21/hts.c:3884:47: style: Redundant condition: !(flags&1). 'flags&1 || (!(flags&1) && *s!=',')' is equivalent to 'flags&1 || *s!=','' [redundantCondition]
htslib-1.21/hts.c:1169:41: style: Condition 'strcmp(o->arg,"store_md")==0' is always false [knownConditionTrueFalse]
htslib-1.21/hts.c:1173:41: style: Condition 'strcmp(o->arg,"store_nm")==0' is always false [knownConditionTrueFalse]
htslib-1.21/hts.c:2530:64: style: Condition 'tid<0' is always false [knownConditionTrueFalse]
htslib-1.21/hts.c:2530:52: note: Assuming that condition 'idx->z.last_tid>=0' is not redundant
htslib-1.21/hts.c:2530:25: note: Assuming that condition 'idx->z.last_tid!=tid' is not redundant
htslib-1.21/hts.c:2530:64: note: Condition 'tid<0' is always false
htslib-1.21/hts.c:2670:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/hts.c:2670:18: note: Calling function 'ed_is_big' returns 0
htslib-1.21/hts.c:2670:18: note: Condition 'ed_is_big()' is always false
htslib-1.21/hts.c:2676:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/hts.c:2676:18: note: Calling function 'ed_is_big' returns 0
htslib-1.21/hts.c:2676:18: note: Condition 'ed_is_big()' is always false
htslib-1.21/hts.c:2682:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
htslib-1.21/htslib/hts.h:1550:15: note: Assignment 'one=1', assigned value is 1
htslib-1.21/hts.c:2682:18: note: Calling function 'ed_is_big' returns 0
htslib-1.21/hts.c:2682:18: note: Condition 'ed_is_big()' is always false
htslib-1.21/hts.c:2915:22: style: Condition 'l->n<0' is always false [knownConditionTrueFalse]
htslib-1.21/hts.c:2914:20: note: Assignment 'l->n=x', assigned value is greater than -1
htslib-1.21/hts.c:2915:22: note: Condition 'l->n<0' is always false
htslib-1.21/hts.c:4068:18: style: Condition '*beg!=-1' is always false [knownConditionTrueFalse]
htslib-1.21/hts.c:4066:29: note: Calling function 'hts_parse_decimal' returns !<=-1
htslib-1.21/hts.c:4066:55: note: Assignment '*beg=hts_parse_decimal(colon+1,&hyphen,flags)-1', assigned value is greater than -2
htslib-1.21/hts.c:4067:14: note: Assuming that condition '*beg<0' is not redundant
htslib-1.21/hts.c:4068:18: note: Condition '*beg!=-1' is always false
htslib-1.21/hts.c:4260:53: style: Condition 'iter->end>beg' is always true [knownConditionTrueFalse]
htslib-1.21/hts.c:4258:41: note: Assuming that condition 'beg>=iter->end' is not redundant
htslib-1.21/hts.c:4260:53: note: Condition 'iter->end>beg' is always true
htslib-1.21/hts.c:4397:32: style: Condition 'iter->i<iter->n_off' is always true [knownConditionTrueFalse]
htslib-1.21/hts.c:4364:25: note: Assuming that condition 'iter->i>=iter->n_off' is not redundant
htslib-1.21/hts.c:4397:32: note: Condition 'iter->i<iter->n_off' is always true
htslib-1.21/test/hts_endian.c:169:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/hts_endian.c:252:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/hts_endian.c:333:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/hts_endian.c:415:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/hts_endian.c:460:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/hts_endian.c:508:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:1168:46: style: Same expression on both sides of '||'. [duplicateExpression]
htslib-1.21/hts.c:1172:46: style: Same expression on both sides of '||'. [duplicateExpression]
htslib-1.21/hts.c:1437:48: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/pileup.c:148:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/pileup.c:196:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/pileup.c:235:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/hts.c:548:30: style:inconclusive: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:544:37: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.21/hts.c:548:30: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.21/hts.c:553:31: style:inconclusive: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:561:38: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.21/hts.c:553:31: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.21/hts.c:1287:35: style:inconclusive: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:452:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'.
htslib-1.21/hts.c:1287:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'.
htslib-1.21/hts.c:1324:33: style:inconclusive: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:438:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'.
htslib-1.21/hts.c:1324:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'.
htslib-1.21/hts.c:1450:27: style:inconclusive: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:629:34: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.21/hts.c:1450:27: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'.
htslib-1.21/hts.c:2045:33: style:inconclusive: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:696:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'.
htslib-1.21/hts.c:2045:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'.
htslib-1.21/hts.c:4107:41: style:inconclusive: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:1180:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'.
htslib-1.21/hts.c:4107:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'.
htslib-1.21/hts.c:4127:39: style:inconclusive: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent]
htslib-1.21/htslib/hts.h:1190:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'.
htslib-1.21/hts.c:4127:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'.
htslib-1.21/hts.c:624:15: style: Local variable 's' shadows outer variable [shadowVariable]
htslib-1.21/hts.c:556:19: note: Shadowed declaration
htslib-1.21/hts.c:624:15: note: Shadow variable
htslib-1.21/hts.c:2910:17: style: Local variable 'j' shadows outer variable [shadowVariable]
htslib-1.21/hts.c:2881:13: note: Shadowed declaration
htslib-1.21/hts.c:2910:17: note: Shadow variable
htslib-1.21/hts.c:3242:21: style: Local variable 'bin' shadows outer variable [shadowVariable]
htslib-1.21/hts.c:3235:19: note: Shadowed declaration
htslib-1.21/hts.c:3242:21: note: Shadow variable
htslib-1.21/hts.c:3394:22: style: Local variable 'off' shadows outer variable [shadowVariable]
htslib-1.21/hts.c:3376:23: note: Shadowed declaration
htslib-1.21/hts.c:3394:22: note: Shadow variable
htslib-1.21/hts.c:4372:36: style: Local variable 'r' shadows outer argument [shadowArgument]
htslib-1.21/hts.c:4272:60: note: Shadowed declaration
htslib-1.21/hts.c:4372:36: note: Shadow variable
htslib-1.21/hts.c:4427:40: style: Local variable 'r' shadows outer argument [shadowArgument]
htslib-1.21/hts.c:4272:60: note: Shadowed declaration
htslib-1.21/hts.c:4427:40: note: Shadow variable
htslib-1.21/hts.c:4443:33: style: Local variable 'tid' shadows outer variable [shadowVariable]
htslib-1.21/hts.c:4275:14: note: Shadowed declaration
htslib-1.21/hts.c:4443:33: note: Shadow variable
htslib-1.21/hts.c:4444:37: style: Local variable 'end' shadows outer variable [shadowVariable]
htslib-1.21/hts.c:4276:20: note: Shadowed declaration
htslib-1.21/hts.c:4444:37: note: Shadow variable
htslib-1.21/hts.c:136:43: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/hts.c:138:38: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/hts.c:140:39: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/hts.c:142:46: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/hts.c:144:41: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/hts.c:146:40: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
htslib-1.21/hts.c:1237:14: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:1455:34: style: Variable 'opts' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:1864:15: style: Variable 'expr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:2485:36: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hts.c:2661:28: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hts.c:2730:17: style: Variable 'lidx' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:2738:29: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:3031:38: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hts.c:3049:17: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:3094:112: style: Parameter 'bidx' can be declared as pointer to const [constParameterPointer]
htslib-1.21/hts.c:3256:13: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:3309:20: style: Variable 'reg1' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:3310:20: style: Variable 'reg2' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:3601:31: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:3700:19: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:4277:20: style: Variable 'found_reg' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:4521:50: error: Uninitialized variables: &key.reg, &key.intervals, &key.count, &key.min_beg, &key.max_end [uninitvar]
htslib-1.21/test/hts_endian.c:149:31: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/pileup.c:81:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/pileup.c:126:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.21/hts.c:3382:23: style: Variable 'unmapped' is assigned a value that is never used. [unreadVariable]
htslib-1.21/hts.c:4366:32: style: Variable 'next_range' is assigned a value that is never used. [unreadVariable]
htslib-1.21/test/pileup_mod.c:157:13: style: Local variable 'n' shadows outer argument [shadowArgument]
htslib-1.21/test/pileup_mod.c:141:47: note: Shadowed declaration
htslib-1.21/test/pileup_mod.c:157:13: note: Shadow variable
htslib-1.21/test/pileup_mod.c:49:32: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/pileup_mod.c:60:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/pileup_mod.c:61:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/pileup_mod.c:91:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/pileup_mod.c:102:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/pileup_mod.c:103:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/pileup_mod.c:140:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/pileup_mod.c:151:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/pileup_mod.c:152:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/pileup_mod.c:161:16: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
htslib-1.21/test/test-bcf-sr.c:49:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-bcf-sr.c:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-bcf-sr.c:147:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:64:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:112:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:156:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:213:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:318:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:901:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:992:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:1064:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:1170:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:1228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:1397:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:1516:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:1581:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:1783:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2005:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2041:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2086:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2115:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2137:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2154:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2174:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2203:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2243:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:2315:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-bcf-translate.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-bcf-translate.c:114:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-bcf-sr.c:77:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test-bcf-sr.c:94:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test-bcf-sr.c:127:26: style: Variable 'loptions' can be declared as const array [constVariable]
htslib-1.21/test/test-parse-reg.c:63:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-parse-reg.c:98:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-parse-reg.c:172:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-parse-reg.c:51:24: style: Parameter 'reg_exp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test-parse-reg.c:72:20: style: Parameter 'fn' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test-regidx.c:50:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:60:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:69:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:128:103: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:162:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:193:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:218:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu32 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:281:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:363:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:417:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:441:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/test/sam.c:443:15: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.21/test/sam.c:442:15: note: First condition
htslib-1.21/test/sam.c:443:15: note: Second condition
htslib-1.21/test/sam.c:444:15: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.21/test/sam.c:443:15: note: First condition
htslib-1.21/test/sam.c:444:15: note: Second condition
htslib-1.21/test/sam.c:445:15: style: The if condition is the same as the previous if condition [duplicateCondition]
htslib-1.21/test/sam.c:444:15: note: First condition
htslib-1.21/test/sam.c:445:15: note: Second condition
htslib-1.21/htslib/khash.h:449:10: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
htslib-1.21/test/sam.c:1214:5: note: Assuming allocation function fails
htslib-1.21/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0
htslib-1.21/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
htslib-1.21/htslib/khash.h:449:10: note: Null pointer dereference
htslib-1.21/htslib/khash.h:449:38: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
htslib-1.21/test/sam.c:1214:5: note: Assuming allocation function fails
htslib-1.21/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0
htslib-1.21/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
htslib-1.21/htslib/khash.h:449:38: note: Null pointer dereference
htslib-1.21/test/sam.c:996:27: warning: Either the condition '!text' is redundant or there is possible null pointer dereference: text. [nullPointerRedundantCheck]
htslib-1.21/test/sam.c:990:9: note: Assuming that condition '!text' is not redundant
htslib-1.21/test/sam.c:996:27: note: Null pointer dereference
htslib-1.21/test/sam.c:1068:34: warning: Either the condition '!text' is redundant or there is possible null pointer dereference: text. [nullPointerRedundantCheck]
htslib-1.21/test/sam.c:1062:13: note: Assuming that condition '!text' is not redundant
htslib-1.21/test/sam.c:1068:34: note: Null pointer dereference
htslib-1.21/test/sam.c:1590:37: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
htslib-1.21/test/sam.c:1585:16: note: Assuming allocation function fails
htslib-1.21/test/sam.c:1585:16: note: Assignment 'fin=fopen(filename,"rb")', assigned value is 0
htslib-1.21/test/sam.c:1590:37: note: Null pointer dereference
htslib-1.21/test/sam.c:1593:21: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
htslib-1.21/test/sam.c:1588:17: note: Assuming allocation function fails
htslib-1.21/test/sam.c:1588:17: note: Assignment 'fout=fopen(tmpfilename,"wb")', assigned value is 0
htslib-1.21/test/sam.c:1593:21: note: Null pointer dereference
htslib-1.21/test/sam.c:1596:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
htslib-1.21/test/sam.c:1588:17: note: Assuming allocation function fails
htslib-1.21/test/sam.c:1588:17: note: Assignment 'fout=fopen(tmpfilename,"wb")', assigned value is 0
htslib-1.21/test/sam.c:1596:12: note: Null pointer dereference
htslib-1.21/htslib/khash.h:449:13: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
htslib-1.21/test/sam.c:1214:5: note: Assuming allocation function fails
htslib-1.21/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0
htslib-1.21/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
htslib-1.21/htslib/khash.h:449:13: note: Null pointer addition
htslib-1.21/test/sam.c:1664:24: style: The comparison 'no_compression != 0' is always false. [knownConditionTrueFalse]
htslib-1.21/test/sam.c:1665:14: style: The comparison 'gzip != 1' is always false. [knownConditionTrueFalse]
htslib-1.21/test/sam.c:1666:14: style: The comparison 'bgzf != 2' is always false. [knownConditionTrueFalse]
htslib-1.21/test/sam.c:763:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:766:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:770:49: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:773:55: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:781:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:784:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:787:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:851:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:956:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:960:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:964:63: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:967:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:970:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:980:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:983:61: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1055:46: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1126:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1128:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1130:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1132:73: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1139:71: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1142:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1145:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1273:64: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1276:81: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1281:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1289:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1297:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1322:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1331:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:1340:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:2248:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
htslib-1.21/test/sam.c:99:39: style: Parameter 'aln' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/sam.c:101:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/sam.c:2310:11: style: Variable 'cig' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/sam.c:48:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.21/test/sam.c:498:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
htslib-1.21/vcf.c:242:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:313:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:336:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:351:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:377:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:710:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:1166:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:1216:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:1511:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:1532:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:1732:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:1761:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:1911:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2198:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2268:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2385:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2468:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2823:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2849:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2957:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:2993:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:3087:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:3319:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:3455:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:3514:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:3908:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:3965:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:4289:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:4649:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:4823:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5100:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5111:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5174:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5333:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5440:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5461:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5483:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5499:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5655:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5662:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5692:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5776:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:5815:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-bcf_set_variant_type.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-regidx.c:92:11: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test-regidx.c:250:11: style: Variable 'beg' can be declared as pointer to const [constVariablePointer]
htslib-1.21/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-1.21/test/test-regidx.c:457:10: note: You might need to cast the function pointer here
htslib-1.21/test/test-regidx.c:307:53: note: Parameter 'chr' can be declared as pointer to const
htslib-1.21/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-1.21/test/test-regidx.c:451:10: note: You might need to cast the function pointer here
htslib-1.21/test/test-regidx.c:311:53: note: Parameter 'chr' can be declared as pointer to const
htslib-1.21/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-1.21/test/test-regidx.c:454:10: note: You might need to cast the function pointer here
htslib-1.21/test/test-regidx.c:315:53: note: Parameter 'chr' can be declared as pointer to const
htslib-1.21/test/test-regidx.c:428:26: style: Variable 'loptions' can be declared as const array [constVariable]
htslib-1.21/test/test-vcf-sweep.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:52:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:112:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:288:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:407:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:435:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:493:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:547:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test-vcf-api.c:586:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/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-1.21/test/test-vcf-api.c:203:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory]
htslib-1.21/test/test-vcf-api.c:202:34: note: Assuming allocation function fails
htslib-1.21/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0
htslib-1.21/test/test-vcf-api.c:203:5: note: Null pointer dereference
htslib-1.21/test/test-vcf-api.c:204:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory]
htslib-1.21/test/test-vcf-api.c:202:34: note: Assuming allocation function fails
htslib-1.21/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0
htslib-1.21/test/test-vcf-api.c:204:5: note: Null pointer dereference
htslib-1.21/test/test-vcf-api.c:205:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory]
htslib-1.21/test/test-vcf-api.c:202:34: note: Assuming allocation function fails
htslib-1.21/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0
htslib-1.21/test/test-vcf-api.c:205:5: note: Null pointer dereference
htslib-1.21/test/test-vcf-api.c:206:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory]
htslib-1.21/test/test-vcf-api.c:202:34: note: Assuming allocation function fails
htslib-1.21/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0
htslib-1.21/test/test-vcf-api.c:206:5: note: Null pointer dereference
htslib-1.21/test/test-vcf-api.c:207:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory]
htslib-1.21/test/test-vcf-api.c:202:34: note: Assuming allocation function fails
htslib-1.21/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0
htslib-1.21/test/test-vcf-api.c:207:5: note: Null pointer dereference
htslib-1.21/test/test-vcf-api.c:208:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory]
htslib-1.21/test/test-vcf-api.c:202:34: note: Assuming allocation function fails
htslib-1.21/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0
htslib-1.21/test/test-vcf-api.c:208:5: note: Null pointer dereference
htslib-1.21/test/test-vcf-api.c:254:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpfa [nullPointerOutOfMemory]
htslib-1.21/test/test-vcf-api.c:253:34: note: Assuming allocation function fails
htslib-1.21/test/test-vcf-api.c:253:20: note: Assignment 'tmpfa=(float*)malloc(2*sizeof(float))', assigned value is 0
htslib-1.21/test/test-vcf-api.c:254:5: note: Null pointer dereference
htslib-1.21/test/test-vcf-api.c:69:44: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test-vcf-api.c:357:17: style: Variable 'tmpia' can be declared as const array [constVariable]
htslib-1.21/test/test_bgzf.c:71:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:81:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:93:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:113:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:125:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:168:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:184:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:194:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:207:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:218:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:238:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:248:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:270:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:281:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:291:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:302:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:318:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:332:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:367:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:408:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:444:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:524:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:590:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:623:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:646:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:741:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:842:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:886:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:931:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:992:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_bgzf.c:1078:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_expr.c:307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_expr.c:101:19: warning: Either the condition 'a' is redundant or there is possible null pointer dereference: a. [nullPointerRedundantCheck]
htslib-1.21/test/test_expr.c:100:9: note: Assuming that condition 'a' is not redundant
htslib-1.21/test/test_expr.c:101:19: note: Null pointer dereference
htslib-1.21/test/test_faidx.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:91:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:104:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:275:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:300:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:325:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:355:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:382:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_faidx.c:445:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/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-1.21/test/test_bgzf.c:518:23: note: Assuming that condition 'pos<sizeof(append_mode)-1' is not redundant
htslib-1.21/test/test_bgzf.c:518:56: note: Array index out of bounds
htslib-1.21/test/test_bgzf.c:519:32: error: Array 'mode[2]' accessed at index 14, which is out of bounds. [arrayIndexOutOfBounds]
htslib-1.21/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-1.21/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-1.21/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-1.21/test/test_bgzf.c:255:36: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:435:35: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:511:34: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:622:33: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:638:41: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:730:39: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:831:34: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:881:41: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:924:37: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_bgzf.c:981:55: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_index.c:39:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_index.c:49:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kfunc.c:43:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kfunc.c:84:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_khash.c:48:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
htslib-1.21/test/test_kstring.c:51:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:102:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:134:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:200:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:275:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:392:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:448:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:470:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_mod.c:120:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_kstring.c:50:13: style: Condition 'val!=0' is always false [knownConditionTrueFalse]
htslib-1.21/test/test_kstring.c:45:11: note: Assignment 'val=0', assigned value is 0
htslib-1.21/test/test_kstring.c:50:13: note: Condition 'val!=0' is always false
htslib-1.21/test/test_kstring.c:310:44: style: Condition 'valm>=5' is always false [knownConditionTrueFalse]
htslib-1.21/test/test_kstring.c:309:26: note: Assignment 'valm=-val', assigned value is less than 1
htslib-1.21/test/test_kstring.c:310:44: note: Condition 'valm>=5' is always false
htslib-1.21/test/test_kstring.c:458:11: style: Variable 'test' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test_mod.c:173:14: style: Variable 'all_mods' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test_nibbles.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_nibbles.c:155:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_realn.c:39:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_realn.c:60:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_nibbles.c:54:17: style: Local variable 'buf' shadows outer variable [shadowVariable]
htslib-1.21/test/test_nibbles.c:76:6: note: Shadowed declaration
htslib-1.21/test/test_nibbles.c:54:17: note: Shadow variable
htslib-1.21/test/test_nibbles.c:69:34: style: Parameter 'nib' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/test_realn.c:45:11: style: Variable 'in_name' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test_realn.c:46:11: style: Variable 'out_name' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test_realn.c:47:11: style: Variable 'ref_name' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test_realn.c:49:10: style: Variable 'modew' can be declared as const array [constVariable]
htslib-1.21/test/test_str2int.c:53:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_str2int.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_str2int.c:160:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_str2int.c:166:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_str2int.c:200:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_str2int.c:217:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/hts_time_funcs.h:168:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_time_funcs.c:44:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_time_funcs.c:58:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/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-1.21/hts_time_funcs.h:139:9: style: Variable 'month_start' can be declared as const array [constVariable]
htslib-1.21/test/thrash_threads1.c:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_view.c:73:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_view.c:212:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/test_view.c:306:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
htslib-1.21/test/thrash_threads3.c:38:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/thrash_threads4.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/thrash_threads4.c:57:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/test/thrash_threads4.c:61:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/test/thrash_threads5.c:40:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/thrash_threads6.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/thrash_threads6.c:94:17: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/test/thrash_threads7.c:87:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
htslib-1.21/test/thrash_threads7.c:45:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
htslib-1.21/test/thrash_threads7.c:44:19: style: Variable 'usecs' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test_view.c:286:11: style: Variable 'out_fn' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/test_view.c:200:29: style: Variable 'r' is assigned a value that is never used. [unreadVariable]
htslib-1.21/textutils.c:169:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/textutils.c:327:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
htslib-1.21/textutils.c:455:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
htslib-1.21/textutils.c:185:23: style: Variable 'lim' can be declared as pointer to const [constVariablePointer]
htslib-1.21/textutils.c:202:40: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
htslib-1.21/textutils.c:228:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
htslib-1.21/textutils.c:238:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
htslib-1.21/textutils.c:456:21: style: Variable 'bufend' can be declared as pointer to const [constVariablePointer]
htslib-1.21/test/usepublic.cpp:64:1: warning: If memory allocation fails, then there is a possible null pointer dereference: kl [nullPointerOutOfMemory]
htslib-1.21/test/usepublic.cpp:64:1: note: Assuming allocation function fails
htslib-1.21/test/usepublic.cpp:64:1: note: Assignment 'kl=(struct kl_intlist_t*)calloc(1,sizeof(struct kl_intlist_t))', assigned value is 0
htslib-1.21/test/usepublic.cpp:64:1: note: Null pointer dereference
htslib-1.21/test/usepublic.cpp:70:1: warning: If memory allocation fails, then there is a possible null pointer dereference: ks [nullPointerOutOfMemory]
htslib-1.21/test/usepublic.cpp:70:1: note: Assuming allocation function fails
htslib-1.21/test/usepublic.cpp:70:1: note: Assignment 'ks=(struct kstream_t*)calloc(1,sizeof(struct kstream_t))', assigned value is 0
htslib-1.21/test/usepublic.cpp:70:1: note: Null pointer dereference
htslib-1.21/test/usepublic.cpp:70:1: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
htslib-1.21/test/usepublic.cpp:70:1: note: Assuming allocation function fails
htslib-1.21/test/usepublic.cpp:70:1: note: Assignment 's=(struct kseq_t*)calloc(1,sizeof(struct kseq_t))', assigned value is 0
htslib-1.21/test/usepublic.cpp:70:1: note: Null pointer dereference
htslib-1.21/htslib/bgzf.h:156:16: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/bgzf.h:157:16: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/bgzf.h:188:16: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/kstring.h:160:12: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/hts.h:1551:16: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/hts.h:1559:6: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/hts.h:1559:32: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/hts.h:1569:6: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/hts.h:1569:32: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/hts.h:1580:6: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/hts.h:1580:32: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/sam.h:1470:18: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/sam.h:1478:21: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/sam.h:1566:29: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/sam.h:1574:30: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/kbitset.h:82:4: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/kbitset.h:106:9: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:30:1: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:46:31: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:55:31: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:59:37: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:68:31: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:80:31: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:100:31: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:118:31: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/khash_str2int.h:131:31: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1121:36: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1537:22: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1545:18: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1577:18: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1624:14: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1627:14: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1630:14: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1633:14: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/vcf.h:1665:14: style: C-style pointer casting [cstyleCast]
htslib-1.21/test/usepublic.cpp:61:1: style: C-style pointer casting [cstyleCast]
htslib-1.21/test/usepublic.cpp:64:1: style: C-style pointer casting [cstyleCast]
htslib-1.21/test/usepublic.cpp:66:1: style: C-style pointer casting [cstyleCast]
htslib-1.21/test/usepublic.cpp:70:1: style: C-style pointer casting [cstyleCast]
htslib-1.21/htslib/kstring.h:407:14: style: The scope of the variable 'm' can be reduced. [variableScope]
htslib-1.21/htslib/khash.h:470:64: performance: Function parameter 'ks' should be passed by const reference. [passedByValue]
htslib-1.21/htslib/khash.h:484:66: performance: Function parameter 'ks' should be passed by const reference. [passedByValue]
htslib-1.21/thread_pool.c:752:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_RECURSIVE [valueFlowBailoutIncompleteVar]
htslib-1.21/thread_pool.c:856:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
htslib-1.21/test/usepublic.cpp:70:1: style: Parameter 'f' can be declared as pointer to const [constParameterPointer]
htslib-1.21/test/usepublic.cpp:61:1: error: Uninitialized variable: val [legacyUninitvar]
htslib-1.21/thread_pool.c:1048:36: style: Condition 'hts_tpool_process_flush(q)!=0' is always false [knownConditionTrueFalse]
htslib-1.21/thread_pool.c:1048:32: note: Calling function 'hts_tpool_process_flush' returns 0
htslib-1.21/thread_pool.c:1048:36: note: Condition 'hts_tpool_process_flush(q)!=0' is always false
htslib-1.21/thread_pool.c:354:47: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
htslib-1.21/thread_pool.c:473:43: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
htslib-1.21/thread_pool.c:815:31: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
htslib-1.21/thread_pool.c:1077:48: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf_sweep.c:82:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf_sweep.c:106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf_sweep.c:174:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
htslib-1.21/vcf.c:601:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition]
htslib-1.21/vcf.c:610:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition]
htslib-1.21/vcf.c:616:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition]
htslib-1.21/vcf.c:1973:78: style: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false [knownConditionTrueFalse]
htslib-1.21/vcf.c:1973:26: note: Calling function 'bcf_enc_vchar' returns 0
htslib-1.21/vcf.c:1973:78: note: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false
htslib-1.21/vcf.c:3350:16: style: Condition 'ret' is always true [knownConditionTrueFalse]
htslib-1.21/vcf_sweep.c:117:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:117:5: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:118:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:118:5: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:118:30: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:118:30: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:119:9: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:119:9: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:120:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:120:5: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:120:29: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:120:29: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:121:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:121:5: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:122:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:122:5: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:122:33: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:122:33: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:123:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:123:5: note: Null pointer dereference
htslib-1.21/vcf_sweep.c:124:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
htslib-1.21/vcf_sweep.c:124:5: note: Null pointer dereference
htslib-1.21/vcf.c:3186:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcf.c:3258:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcf.c:3291:43: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcf.c:3616:32: portability: Casting between signed int * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcf_sweep.c:58:45: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf_sweep.c:64:11: style: Variable 't' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf_sweep.c:189:39: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:5846:52: style: Same value in both branches of ternary operator. [duplicateValueTernary]
htslib-1.21/vcf.c:183:35: style:inconclusive: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:571:39: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.21/vcf.c:183:35: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.21/vcf.c:183:50: style:inconclusive: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:571:56: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'.
htslib-1.21/vcf.c:183:50: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'.
htslib-1.21/vcf.c:1264:31: style:inconclusive: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:596:35: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.21/vcf.c:1264:31: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.21/vcf.c:1274:32: style:inconclusive: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:621:36: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.21/vcf.c:1274:32: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.21/vcf.c:1339:31: style:inconclusive: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:599:35: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.21/vcf.c:1339:31: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'.
htslib-1.21/vcf.c:1339:48: style:inconclusive: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:599:50: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'.
htslib-1.21/vcf.c:1339:48: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'.
htslib-1.21/vcf.c:1472:34: style:inconclusive: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:340:38: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/vcf.c:1472:34: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/vcf.c:1529:28: style:inconclusive: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:376:32: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/vcf.c:1529:28: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/vcf.c:1949:45: style:inconclusive: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:506:49: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'.
htslib-1.21/vcf.c:1949:45: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'.
htslib-1.21/vcf.c:2191:24: style:inconclusive: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:452:28: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/vcf.c:2191:24: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'.
htslib-1.21/vcf.c:2448:56: style:inconclusive: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:646:60: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'.
htslib-1.21/vcf.c:2448:56: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'.
htslib-1.21/vcf.c:4266:37: style:inconclusive: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:1203:41: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.21/vcf.c:4266:37: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'.
htslib-1.21/vcf.c:4266:44: style:inconclusive: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:1203:50: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'.
htslib-1.21/vcf.c:4266:44: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'.
htslib-1.21/vcf.c:4643:73: style:inconclusive: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcf.h:791:77: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'.
htslib-1.21/vcf.c:4643:73: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'.
htslib-1.21/vcf.c:767:17: style: Local variable 'k' shadows outer variable [shadowVariable]
htslib-1.21/vcf.c:742:13: note: Shadowed declaration
htslib-1.21/vcf.c:767:17: note: Shadow variable
htslib-1.21/vcf.c:3027:13: style: Local variable 'j' shadows outer variable [shadowVariable]
htslib-1.21/vcf.c:2983:9: note: Shadowed declaration
htslib-1.21/vcf.c:3027:13: note: Shadow variable
htslib-1.21/vcf.c:4127:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/vcf.c:3959:9: note: Shadowed declaration
htslib-1.21/vcf.c:4127:13: note: Shadow variable
htslib-1.21/vcf.c:4902:16: style: Local variable 'samples' shadows outer argument [shadowArgument]
htslib-1.21/vcf.c:4843:53: note: Shadowed declaration
htslib-1.21/vcf.c:4902:16: note: Shadow variable
htslib-1.21/vcf.c:4931:17: style: Local variable 'k' shadows outer variable [shadowVariable]
htslib-1.21/vcf.c:4904:13: note: Shadowed declaration
htslib-1.21/vcf.c:4931:17: note: Shadow variable
htslib-1.21/vcf.c:275:38: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:329:34: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:426:35: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:512:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:522:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:533:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:945:50: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:986:36: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:1159:38: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:1371:17: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:1414:20: style: Variable 'dsize' can be declared as const array [constVariable]
htslib-1.21/vcf.c:1673:57: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:1729:64: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:1826:19: style: Variable 'id_tmp' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:1959:40: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:1995:21: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:2015:11: style: Variable 'shared_ori' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:2117:24: style: Variable 'fmt' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:2303:23: style: Variable 'tab' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:2339:25: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:2515:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:2643:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:2731:19: style: Variable 'p_end' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:2818:47: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:2891:45: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:2916:21: style: Variable 'meta' can be declared as const array [constVariable]
htslib-1.21/vcf.c:2928:15: style: Variable 'r_start' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:3040:24: style: Variable 'jfmt' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:3056:46: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:3644:23: style: Variable 't' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4053:27: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4100:29: style: Variable 'missing' can be declared as const array [constVariable]
htslib-1.21/vcf.c:4161:31: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4232:56: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:4402:49: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:4505:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4518:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4527:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4528:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4598:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4611:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4620:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4621:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4951:59: style: Parameter 'imap' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:4962:24: style: Variable 'f' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:5479:62: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
htslib-1.21/vcf.c:5803:18: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcf.c:4429:35: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
htslib-1.21/vcf.c:1008:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
htslib-1.21/vcf.c:1388:14: style: Variable 'hrec' is assigned a value that is never used. [unreadVariable]
htslib-1.21/vcf.c:2517:17: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
htslib-1.21/vcf.c:2517:34: style: Variable 'min' is assigned a value that is never used. [unreadVariable]
htslib-1.21/vcf.c:3409:22: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
htslib-1.21/vcf.c:3433:19: style: Variable 'max_n_flt' is assigned a value that is never used. [unreadVariable]
htslib-1.21/vcfutils.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcfutils.c:216:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcfutils.c:286:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
htslib-1.21/vcfutils.c:463:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcfutils.c:497:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcfutils.c:775:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcfutils.c:829:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
htslib-1.21/vcfutils.c:134:55: style:inconclusive: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcfutils.h:117:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'.
htslib-1.21/vcfutils.c:134:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'.
htslib-1.21/vcfutils.c:134:66: style:inconclusive: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcfutils.h:117:65: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'.
htslib-1.21/vcfutils.c:134:66: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'.
htslib-1.21/vcfutils.c:241:67: style:inconclusive: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. [funcArgNamesDifferent]
htslib-1.21/htslib/vcfutils.h:61:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'.
htslib-1.21/vcfutils.c:241:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'.
htslib-1.21/vcfutils.c:43:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/vcfutils.c:34:9: note: Shadowed declaration
htslib-1.21/vcfutils.c:43:13: note: Shadow variable
htslib-1.21/vcfutils.c:96:13: style: Local variable 'i' shadows outer variable [shadowVariable]
htslib-1.21/vcfutils.c:34:9: note: Shadowed declaration
htslib-1.21/vcfutils.c:96:13: note: Shadow variable
htslib-1.21/vcfutils.c:579:17: style: Local variable 'size' shadows outer variable [shadowVariable]
htslib-1.21/vcfutils.c:563:13: note: Shadowed declaration
htslib-1.21/vcfutils.c:579:17: note: Shadow variable
htslib-1.21/vcfutils.c:44:18: style: Variable 'ac_ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:462:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:463:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:496:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:497:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:624:56: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:774:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:775:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:828:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
htslib-1.21/vcfutils.c:829:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
diff:
2.17.0 htslib-1.21/cram/cram_codecs.c:3108:33: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     htslib-1.21/cram/cram_codecs.c:3107:23: note: Assuming allocation function fails
     htslib-1.21/cram/cram_codecs.c:3107:23: note: Assignment 'tmp=malloc(6*c->u.e_huffman.nvals+16)', assigned value is 0
     htslib-1.21/cram/cram_codecs.c:3108:33: note: Null pointer addition
head htslib-1.21/cram/cram_codecs.c:3108:33: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     htslib-1.21/cram/cram_codecs.c:3107:23: note: Assuming allocation function fails
     htslib-1.21/cram/cram_codecs.c:3107:23: note: Assignment 'tmp=malloc(6*c->u.e_huffman.nvals+16)', assigned value is 0
     htslib-1.21/cram/cram_codecs.c:3108:33: note: Null pointer addition
head htslib-1.21/hfile_s3.c:127:2: error: #error No HMAC() routine found by configure [preprocessorErrorDirective]
head htslib-1.21/hts.c:4068:18: style: Condition '*beg!=-1' is always false [knownConditionTrueFalse]
     htslib-1.21/hts.c:4066:29: note: Calling function 'hts_parse_decimal' returns !<=-1
     htslib-1.21/hts.c:4066:55: note: Assignment '*beg=hts_parse_decimal(colon+1,&hyphen,flags)-1', assigned value is greater than -2
     htslib-1.21/hts.c:4067:14: note: Assuming that condition '*beg<0' is not redundant
     htslib-1.21/hts.c:4068:18: note: Condition '*beg!=-1' is always false
head htslib-1.21/htslib/hts.h:1559:32: style: C-style pointer casting [cstyleCast]
head htslib-1.21/htslib/hts.h:1569:32: style: C-style pointer casting [cstyleCast]
head htslib-1.21/htslib/hts.h:1580:32: style: C-style pointer casting [cstyleCast]
2.17.0 htslib-1.21/htslib/khash.h:449:13: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     htslib-1.21/faidx.c:100:28: note: Assuming allocation function fails
     htslib-1.21/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0
     htslib-1.21/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0
     htslib-1.21/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
     htslib-1.21/htslib/khash.h:449:13: note: Null pointer addition
2.17.0 htslib-1.21/htslib/khash.h:449:13: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     htslib-1.21/test/sam.c:1214:5: note: Assuming allocation function fails
     htslib-1.21/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0
     htslib-1.21/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
     htslib-1.21/htslib/khash.h:449:13: note: Null pointer addition
head htslib-1.21/htslib/khash.h:449:13: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     htslib-1.21/faidx.c:100:28: note: Assuming allocation function fails
     htslib-1.21/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0
     htslib-1.21/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0
     htslib-1.21/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
     htslib-1.21/htslib/khash.h:449:13: note: Null pointer addition
head htslib-1.21/htslib/khash.h:449:13: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     htslib-1.21/test/sam.c:1214:5: note: Assuming allocation function fails
     htslib-1.21/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0
     htslib-1.21/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
     htslib-1.21/htslib/khash.h:449:13: note: Null pointer addition
head htslib-1.21/htslib/khash.h:449:38: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
     htslib-1.21/faidx.c:100:28: note: Assuming allocation function fails
     htslib-1.21/faidx.c:100:28: note: Assignment 'name_key=strdup(name)', assigned value is 0
     htslib-1.21/faidx.c:102:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0
     htslib-1.21/faidx.c:76:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
     htslib-1.21/htslib/khash.h:449:38: note: Null pointer dereference
head htslib-1.21/htslib/khash.h:449:38: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
     htslib-1.21/test/sam.c:1214:5: note: Assuming allocation function fails
     htslib-1.21/test/sam.c:1214:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0
     htslib-1.21/test/sam.c:48:1: note: Calling function '__ac_FNV1a_hash_string', 1st argument 'key' value is 0
     htslib-1.21/htslib/khash.h:449:38: note: Null pointer dereference
head htslib-1.21/sam.c:5725:18: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
     htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
     htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
     htslib-1.21/sam.c:5725:18: note: Null pointer dereference
head htslib-1.21/sam.c:5725:40: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
     htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
     htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
     htslib-1.21/sam.c:5725:40: note: Null pointer dereference
head htslib-1.21/sam.c:5726:21: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
     htslib-1.21/sam.c:5723:29: note: Assuming allocation function fails
     htslib-1.21/sam.c:5723:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0
     htslib-1.21/sam.c:5726:21: note: Null pointer dereference
head htslib-1.21/sam.c:6276:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
     htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
     htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
     htslib-1.21/sam.c:6276:24: note: Null pointer dereference
head htslib-1.21/sam.c:6277:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory]
     htslib-1.21/sam.c:6265:30: note: Assuming allocation function fails
     htslib-1.21/sam.c:6265:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0
     htslib-1.21/sam.c:6277:24: note: Null pointer dereference
head htslib-1.21/vcf_sweep.c:118:30: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
     htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
     htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
     htslib-1.21/vcf_sweep.c:118:30: note: Null pointer dereference
head htslib-1.21/vcf_sweep.c:120:29: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
     htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
     htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
     htslib-1.21/vcf_sweep.c:120:29: note: Null pointer dereference
head htslib-1.21/vcf_sweep.c:122:33: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
     htslib-1.21/vcf_sweep.c:116:44: note: Assuming allocation function fails
     htslib-1.21/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
     htslib-1.21/vcf_sweep.c:122:33: note: Null pointer dereference


DONE