2026-01-11 14:30 ftp://ftp.de.debian.org/debian/pool/main/r/r-bioc-rhtslib/r-bioc-rhtslib_3.2.0+dfsg.orig.tar.xz cppcheck-options: --library=posix --library=gnu --library=bsd --library=openssl --library=zlib --library=libcurl --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j8 platform: Linux-6.17.12+deb14-amd64-x86_64-with-glibc2.42 python: 3.13.11 client-version: 1.3.69 compiler: g++ (Debian 15.2.0-12) 15.2.0 cppcheck: head 2.19.0 head-info: 34b9c45c (2026-01-11 10:36:15 +0100) count: 871 1677 elapsed-time: 2.4 8.2 head-timing-info: old-timing-info: head results: Rhtslib/inst/include/bam_plbuf.c:47:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] Rhtslib/inst/include/bam_plbuf.c:46:17: note: Assuming allocation function fails Rhtslib/inst/include/bam_plbuf.c:46:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0 Rhtslib/inst/include/bam_plbuf.c:47:5: note: Null pointer dereference Rhtslib/inst/include/bam_plbuf.c:48:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] Rhtslib/inst/include/bam_plbuf.c:46:17: note: Assuming allocation function fails Rhtslib/inst/include/bam_plbuf.c:46:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0 Rhtslib/inst/include/bam_plbuf.c:48:5: note: Null pointer dereference Rhtslib/inst/include/bam_plbuf.c:49:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] Rhtslib/inst/include/bam_plbuf.c:46:17: note: Assuming allocation function fails Rhtslib/inst/include/bam_plbuf.c:46:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0 Rhtslib/inst/include/bam_plbuf.c:49:5: note: Null pointer dereference Rhtslib/inst/include/sam_utils.h:37:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_SET_INIT_INT is a macro then please configure it. [unknownMacro] Rhtslib/inst/include/bedidx.c:39:1: error: There is an unknown macro here somewhere. Configuration is required. If KSTREAM_INIT is a macro then please configure it. [unknownMacro] Rhtslib/inst/include/sam_opts.c:71:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/inst/include/sam_opts.c:140:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] Rhtslib/inst/include/bam.c:72:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] Rhtslib/inst/include/sam_opts.c:111:18: style: Variable 'opts' can be declared as pointer to const [constVariablePointer] Rhtslib/inst/include/bam.c:35:40: style:inconclusive: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. [funcArgNamesDifferent] Rhtslib/inst/include/bam.h:32:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. Rhtslib/inst/include/bam.c:35:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. Rhtslib/src/htslib-1.18/htslib/kstring.h:159:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:238:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:247:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:263:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:272:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:313:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:369:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/kstring.h:385:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/hfile.h:281:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bufsiz [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzip.c:52:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzip.c:60:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzip.c:67:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzip.c:102:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzip.c:165:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/sam.h:259:25: error: syntax error [syntaxError] Rhtslib/src/htslib-1.18/cram/mFILE.c:157:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/cram/mFILE.c:182:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/cram/mFILE.c:198:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/cram/mFILE.c:463:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/vcf.h:1213:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/vcf.h:1316:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:219:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:240:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:306:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:325:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:332:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:375:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/cram/string_alloc.c:121:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/cram/open_trace_file.c:195:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/cram/mFILE.c:520:13: style: Condition 'len!=size*nmemb' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/cram/mFILE.c:511:9: note: len is assigned 'size*nmemb<=mf->size-mf->offset?size*nmemb:mf->size-mf->offset' here. Rhtslib/src/htslib-1.18/cram/mFILE.c:514:9: note: Assuming condition is false Rhtslib/src/htslib-1.18/cram/mFILE.c:520:13: note: Condition 'len!=size*nmemb' is always true Rhtslib/src/htslib-1.18/cram/mFILE.c:264:47: style:inconclusive: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/cram/mFILE.h:64:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. Rhtslib/src/htslib-1.18/cram/mFILE.c:264:47: note: Function 'mfreopen' argument 2 names different: declaration 'mode' definition 'mode_str'. Rhtslib/src/htslib-1.18/cram/mFILE.c:471:20: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/cram/mFILE.c:494:18: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/cram/mFILE.c:527:22: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/bgzf.c:370:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:411:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:480:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:507:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:529:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:545:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:1094:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:1537:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:1834:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:2363:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:2394:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:2461:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:2501:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/errmod.c:93:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/hts.h:1544:12: style: Return value '!(*((char*)(&one)))' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/htslib/hts.h:1544:12: note: Return value '!(*((char*)(&one)))' is always false Rhtslib/src/htslib-1.18/cram/open_trace_file.c:131:31: style: Condition 'i>0' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/cram/open_trace_file.c:131:20: note: Assuming that condition 'i==0' is not redundant Rhtslib/src/htslib-1.18/cram/open_trace_file.c:131:31: note: Condition 'i>0' is always true Rhtslib/src/htslib-1.18/cram/open_trace_file.c:203:38: style: Checking if unsigned expression 'mfwrite(buf,len,1,mf)' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/cram/open_trace_file.c:229:50: style: Parameter 'dirname' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/cram/open_trace_file.c:232:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/cram/open_trace_file.c:330:48: style: Parameter 'path' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/cram/open_trace_file.c:330:60: style: Parameter 'relative_to' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htslib/hfile.h:130:33: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htslib/hfile.h:151:34: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htslib/kstring.h:180:39: style: Parameter 's' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htslib/kstring.h:196:40: style: Parameter 's' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/faidx.c:412:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/faidx.c:496:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/faidx.c:586:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/faidx.c:699:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_gcs.c:75:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzip.c:217:24: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/bgzip.c:216:36: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/bgzip.c:216:36: note: Assignment 'name=malloc(strlen(argv[optind])+5)', assigned value is 0 Rhtslib/src/htslib-1.18/bgzip.c:217:24: note: Null pointer dereference Rhtslib/src/htslib-1.18/bgzip.c:218:24: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/bgzip.c:216:36: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/bgzip.c:216:36: note: Assignment 'name=malloc(strlen(argv[optind])+5)', assigned value is 0 Rhtslib/src/htslib-1.18/bgzip.c:218:24: note: Null pointer dereference Rhtslib/src/htslib-1.18/bgzip.c:438:17: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/bgzip.c:437:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/bgzip.c:437:30: note: Assignment 'name=strdup(argv[optind])', assigned value is 0 Rhtslib/src/htslib-1.18/bgzip.c:438:17: note: Null pointer dereference Rhtslib/src/htslib-1.18/bgzip.c:428:45: style: Variable 'ext' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile_s3.c:126:2: error: #error No HMAC() routine found by configure [preprocessorErrorDirective] Rhtslib/src/htslib-1.18/hfile.c:155:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:185:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:228:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:238:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:284:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:318:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:358:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:369:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:380:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:404:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:420:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:441:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:485:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:497:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:537:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:548:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:593:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:608:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:643:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:713:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:739:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:772:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:810:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:856:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:905:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:1019:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile.c:1121:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_gcs.c:104:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] Rhtslib/src/htslib-1.18/hfile_gcs.c:105:24: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] Rhtslib/src/htslib-1.18/hfile_gcs.c:112:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] Rhtslib/src/htslib-1.18/textutils_internal.h:345:19: style: Variable 'D' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/errmod.c:34:1: style: Parameter 'array' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:323:48: style:inconclusive: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/bcf_sr_sort.h:103:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. Rhtslib/src/htslib-1.18/bcf_sr_sort.c:323:48: note: Function 'bcf_sr_sort_set_active' argument 2 names different: declaration 'i' definition 'idx'. Rhtslib/src/htslib-1.18/bcf_sr_sort.c:330:48: style:inconclusive: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/bcf_sr_sort.h:104:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. Rhtslib/src/htslib-1.18/bcf_sr_sort.c:330:48: note: Function 'bcf_sr_sort_add_active' argument 2 names different: declaration 'i' definition 'idx'. Rhtslib/src/htslib-1.18/bcf_sr_sort.c:583:85: style:inconclusive: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/bcf_sr_sort.h:102:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. Rhtslib/src/htslib-1.18/bcf_sr_sort.c:583:85: note: Function 'bcf_sr_sort_next' argument 4 names different: declaration 'pos' definition 'min_pos'. Rhtslib/src/htslib-1.18/bcf_sr_sort.c:42:46: style: Parameter 'bs1' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:42:62: style: Parameter 'bs2' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:223:10: style: Variable 'jmat' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:428:24: style: Variable 'var' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/bcf_sr_sort.c:540:19: style: Variable 'vset' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htslib/khash_str2int.h:68:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htslib/khash_str2int.h:131:23: style: Variable 'hash' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile_libcurl.c:131:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOSYS [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:160:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:240:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EBADF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:282:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:315:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:329:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:370:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:513:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:568:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:701:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLM_OK [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:750:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_WRITEFUNC_PAUSE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:767:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:826:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:870:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_READFUNC_PAUSE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:889:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:934:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:1016:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:1134:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:1188:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:1436:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_libcurl.c:1521:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_GLOBAL_ALL [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:157:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:170:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:216:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:256:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_CUSTOMREQUEST [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:322:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_POST [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:404:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_UPLOAD [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:440:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:506:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLINFO_RESPONSE_CODE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:572:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:613:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_URL [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:649:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:682:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:779:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:804:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:826:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hfile_s3_write.c:859:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_GLOBAL_ALL [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htslib/hts_expr.h:80:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hts_expr.c:268:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hts_expr.c:292:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hts_expr.c:751:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REG_EXTENDED [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/hts_expr.c:879:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/c_simple_model.h:123:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Freq [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:883:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:1130:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/bgzf.c:1899:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] Rhtslib/src/htslib-1.18/bgzf.c:2551:27: style: Expression is always true because 'else if' condition is opposite to previous condition at line 2550. [multiCondition] Rhtslib/src/htslib-1.18/bgzf.c:2550:22: note: first condition Rhtslib/src/htslib-1.18/bgzf.c:2551:27: note: else if condition is opposite to first condition Rhtslib/src/htslib-1.18/bgzf.c:332:9: style: Condition '!ed_is_big()' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/bgzf.c:332:19: note: Calling function 'ed_is_big' returns 0 Rhtslib/src/htslib-1.18/bgzf.c:332:9: note: Condition '!ed_is_big()' is always true Rhtslib/src/htslib-1.18/bgzf.c:2339:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/bgzf.c:2339:18: note: Calling function 'ed_is_big' returns 0 Rhtslib/src/htslib-1.18/bgzf.c:2339:18: note: Condition 'ed_is_big()' is always false Rhtslib/src/htslib-1.18/bgzf.c:2435:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/bgzf.c:2435:18: note: Calling function 'ed_is_big' returns 0 Rhtslib/src/htslib-1.18/bgzf.c:2435:18: note: Condition 'ed_is_big()' is always false Rhtslib/src/htslib-1.18/hfile_s3_write.c:165:38: style: Parameter 'start_tag' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:165:55: style: Parameter 'end_tag' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:167:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:286:59: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:371:55: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:584:61: style: Parameter 'head' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:584:78: style: Parameter 'resp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:662:64: style: Parameter 'auth' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile_s3_write.c:798:22: style: Variable 'args2' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile.c:593:17: style: Condition 'ret<0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/hfile.c:582:15: note: Assignment 'ret=0', assigned value is 0 Rhtslib/src/htslib-1.18/hfile.c:593:17: note: Condition 'ret<0' is always false Rhtslib/src/htslib-1.18/hfile.c:594:18: style: Condition 'ret<0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/hfile.c:582:15: note: Assignment 'ret=0', assigned value is 0 Rhtslib/src/htslib-1.18/hfile.c:594:18: note: Condition 'ret<0' is always false Rhtslib/src/htslib-1.18/hfile.c:1012:57: style: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/hfile.c:1012:39: note: Calling function 'try_exe_add_scheme_handler' returns -1 Rhtslib/src/htslib-1.18/hfile.c:1012:57: note: Condition 'try_exe_add_scheme_handler(scheme,handler)!=0' is always true Rhtslib/src/htslib-1.18/bgzf.c:1229:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/bgzf.c:535:25: style:inconclusive: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/bgzf.h:124:36: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. Rhtslib/src/htslib-1.18/bgzf.c:535:25: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. Rhtslib/src/htslib-1.18/bgzf.c:612:25: style:inconclusive: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/bgzf.h:353:29: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. Rhtslib/src/htslib-1.18/bgzf.c:612:25: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. Rhtslib/src/htslib-1.18/bgzf.c:2108:40: style:inconclusive: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/bgzf.h:283:44: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. Rhtslib/src/htslib-1.18/bgzf.c:2108:40: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. Rhtslib/src/htslib-1.18/bgzf.c:2215:46: style:inconclusive: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/bgzf.h:236:50: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. Rhtslib/src/htslib-1.18/bgzf.c:2215:46: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. Rhtslib/src/htslib-1.18/bgzf.c:1159:17: style: Local variable 'ret' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/bgzf.c:1140:13: note: Shadowed declaration Rhtslib/src/htslib-1.18/bgzf.c:1159:17: note: Shadow variable Rhtslib/src/htslib-1.18/hfile.c:1267:26: style:inconclusive: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hfile.h:74:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. Rhtslib/src/htslib-1.18/hfile.c:1267:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. Rhtslib/src/htslib-1.18/hfile.c:1295:27: style:inconclusive: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hfile.h:95:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. Rhtslib/src/htslib-1.18/hfile.c:1295:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. Rhtslib/src/htslib-1.18/hfile.c:1315:46: style:inconclusive: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hfile.h:110:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. Rhtslib/src/htslib-1.18/hfile.c:1315:46: note: Function 'haddextension' argument 4 names different: declaration 'extension' definition 'new_extension'. Rhtslib/src/htslib-1.18/hfile.c:161:50: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile.c:233:11: style: Variable 'found' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile.c:566:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile.c:580:28: 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] Rhtslib/src/htslib-1.18/hfile.c:614:33: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/hfile.c:580:28: note: Parameter 'fpv' can be declared as pointer to const Rhtslib/src/htslib-1.18/hfile.c:600:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile.c:770:30: 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] Rhtslib/src/htslib-1.18/hfile.c:783:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/hfile.c:770:30: note: Parameter 'fpv' can be declared as pointer to const Rhtslib/src/htslib-1.18/hfile.c:776:29: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'mem_close' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback] Rhtslib/src/htslib-1.18/hfile.c:783:33: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/hfile.c:776:29: note: Parameter 'fpv' can be declared as pointer to const Rhtslib/src/htslib-1.18/hfile.c:854:35: style: Parameter 'file' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/hfile.c:1253:31: style: Variable 'p' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/bgzf.c:1233:18: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/bgzf.c:2282:24: style: Variable 'buf' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/bgzf.c:2571:24: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/bgzf.c:2577:39: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/faidx.c:218:31: style: Condition 'c!='\n'' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/faidx.c:216:27: note: Assuming that condition 'c=='+'' is not redundant Rhtslib/src/htslib-1.18/faidx.c:218:31: note: Condition 'c!='\n'' is always true Rhtslib/src/htslib-1.18/faidx.c:1107:34: style: Condition 'p_beg_i<=p_end_i' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/faidx.c:1107:19: note: Assuming that condition 'p_beg_i<0' is not redundant Rhtslib/src/htslib-1.18/faidx.c:1098:44: note: Assuming that condition 'p_end_i<0' is not redundant Rhtslib/src/htslib-1.18/faidx.c:1107:34: note: Condition 'p_beg_i<=p_end_i' is always true Rhtslib/src/htslib-1.18/hfile.c:1353:9: style: struct member 'knetFile_s::type' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/htslib/khash.h:401:24: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/faidx.c:77:28: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/faidx.c:77:28: note: Assignment 'name_key=strdup(name)', assigned value is 0 Rhtslib/src/htslib-1.18/faidx.c:79:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0 Rhtslib/src/htslib-1.18/faidx.c:53:1: note: Calling function '__ac_X31_hash_string', 1st argument 'key' value is 0 Rhtslib/src/htslib-1.18/htslib/khash.h:401:24: note: Null pointer dereference Rhtslib/src/htslib-1.18/faidx.c:119:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/faidx.c:118:27: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/faidx.c:118:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0 Rhtslib/src/htslib-1.18/faidx.c:119:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/faidx.c:120:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/faidx.c:118:27: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/faidx.c:118:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0 Rhtslib/src/htslib-1.18/faidx.c:120:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/hfile.c:1355:11: style: struct member 'knetFile_s::host' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1355:18: style: struct member 'knetFile_s::port' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1356:9: style: struct member 'knetFile_s::ctrl_fd' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1356:18: style: struct member 'knetFile_s::pasv_ip' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1356:30: style: struct member 'knetFile_s::pasv_port' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1356:41: style: struct member 'knetFile_s::max_response' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/faidx.c:705:24: style: Checking if unsigned expression 'val->line_blen' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/hfile.c:1356:55: style: struct member 'knetFile_s::no_reconnect' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/faidx.c:780:59: style:inconclusive: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/faidx.h:201:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:780:59: note: Function 'fai_line_length' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:792:51: style:inconclusive: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/faidx.h:192:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:792:51: note: Function 'fai_fetch64' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:805:49: style:inconclusive: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/faidx.h:190:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:805:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:813:55: style:inconclusive: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/faidx.h:217:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:813:55: note: Function 'fai_fetchqual64' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:825:53: style:inconclusive: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/faidx.h:215:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/faidx.c:825:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. Rhtslib/src/htslib-1.18/hfile.c:1356:69: style: struct member 'knetFile_s::is_ready' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1357:11: style: struct member 'knetFile_s::response' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/faidx.c:865:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/hfile.c:1357:22: style: struct member 'knetFile_s::retr' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1357:29: style: struct member 'knetFile_s::size_cmd' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1358:13: style: struct member 'knetFile_s::seek_offset' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1359:13: style: struct member 'knetFile_s::file_size' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/hfile.c:1360:11: style: struct member 'knetFile_s::path' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/faidx.c:1100:15: error: Memory is allocated but not initialized: seq [uninitdata] Rhtslib/src/htslib-1.18/hfile.c:1360:18: style: struct member 'knetFile_s::http_host' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:207:100: style:inconclusive: Function 'hts_unpack' argument 6 names different: declaration 'map' definition 'p'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.h:80:100: note: Function 'hts_unpack' argument 6 names different: declaration 'map' definition 'p'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:207:100: note: Function 'hts_unpack' argument 6 names different: declaration 'map' definition 'p'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:56:28: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:161:34: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:207:30: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:207:100: style: Parameter 'p' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:274:22: style: Variable 'w' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:316:22: style: Variable 'w' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:347:31: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:347:101: style: Parameter 'p' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/pack.c:114:47: style: Variable 'x' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/hfile_libcurl.c:797:23: style: Condition 'bytes1000' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:1058:18: style:inconclusive: Same expression used in consecutive assignments of 'tmp1_size' and 'tmp2_size'. [duplicateAssignExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:1059:18: note: Same expression used in consecutive assignments of 'tmp1_size' and 'tmp2_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:1058:18: note: Same expression used in consecutive assignments of 'tmp1_size' and 'tmp2_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:933:70: style:inconclusive: Function 'arith_uncompress_to' argument 4 names different: declaration 'out_sz' definition 'out_size'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.h:52:70: note: Function 'arith_uncompress_to' argument 4 names different: declaration 'out_sz' definition 'out_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:933:70: note: Function 'arith_uncompress_to' argument 4 names different: declaration 'out_sz' definition 'out_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:745:17: style: Local variable 'j' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:718:16: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:745:17: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:1099:22: style: Local variable 'osz' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:1027:18: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:1099:22: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:98:49: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:163:49: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:409:53: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:534:53: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:694:20: style: Variable 'out_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:752:17: style: Variable 'm' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:934:20: style: Variable 'in_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/utils.h:79:64: style: Parameter 'outN' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/utils.h:206:30: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/utils.h:251:30: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/utils.h:283:20: style: Variable 'in_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/c_range_coder.h:43:45: style: Parameter 'rc' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/c_range_coder.h:44:44: style: Parameter 'rc' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/c_range_coder.h:96:48: style: Parameter 'rc' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:445:24: style: Variable 'last' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/arith_dynamic.c:847:21: style: Variable 'do_pack' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/utils.c:183:31: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:87:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/entropy.c:93:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:138:21: style: Condition '!rle' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:134:17: note: Assuming that condition 'rle' is not redundant Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:138:21: note: Condition '!rle' is always true Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:400:9: style: Condition '!syms' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:484:25: style: Condition '!rle_j' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:480:21: note: Assuming that condition 'rle_j' is not redundant Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:484:25: note: Condition '!rle_j' is always true Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:639:9: style: Condition '!D' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:203:21: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:203:21: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:68:13: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:156:13: error: Common realloc mistake: 'b' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:157:13: error: Common realloc mistake: 'bu' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:158:13: error: Common realloc mistake: 'bc' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:532:8: style: Redundant initialization for 'l3'. The initialized value is overwritten before it is read. [redundantInitialization] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:529:22: note: l3 is initialized Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:532:8: note: l3 is overwritten Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:274:29: style: Checking if unsigned expression 'in_size' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/htscodecs/tests/arith_dynamic_test.c:146:39: style: Variable 'out_sz' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:78:25: style: Variable 'out_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:176:24: style: Variable 's3' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:177:24: style: Variable 's2' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:178:24: style: Variable 's1' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:179:24: style: Variable 's0' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:472:14: style: Variable 'F_i_' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:545:24: style: Variable 's3' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:546:24: style: Variable 's2' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:547:24: style: Variable 's1' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static.c:548:24: style: Variable 's0' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_byte.h:109:44: style: Parameter 'r' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_byte.h:141:46: style: Parameter 'r' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_byte.h:343:14: style: Variable 'm' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_byte.h:544:77: style: Parameter 'ptr_end' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/tests/entropy.c:182:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/tests/entropy.c:182:17: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/tests/entropy.c:76:13: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/entropy.c:131:11: style: Variable 'codec' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/tokenise_name3.c:185:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:101:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FQZ_VERS [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:235:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:398:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:84:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:99:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:273:29: error: Invalid fputc() argument nr 1. A non-boolean value is required. [invalidFunctionArgBool] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:65:13: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:162:13: error: Common realloc mistake: 'b' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:179:17: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:179:17: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:179:63: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:179:63: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:180:31: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:180:31: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:181:17: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:181:17: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:181:37: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:181:37: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:181:48: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:181:48: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:17: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assignment 'bu=malloc(nb*sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:17: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:45: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:45: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:56: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:56: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:67: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assignment 'bu=malloc(nb*sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:187:67: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:193:32: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assignment 'bu=malloc(nb*sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:193:32: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:193:61: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assignment 'bu=malloc(nb*sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:193:61: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:195:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:172:24: note: Assignment 'bc=malloc(nb*sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:195:22: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:196:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:173:24: note: Assignment 'bu=malloc(nb*sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:196:22: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:267:29: style: Checking if unsigned expression 'in_size' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static_test.c:152:39: style: Variable 'out_sz' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/tests/tokenise_name3_test.c:121:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/tokenise_name3_test.c:180:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:238:21: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:238:21: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:65:13: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:185:17: error: Common realloc mistake: 'b' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:186:17: error: Common realloc mistake: 'bu' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:187:17: error: Common realloc mistake: 'bc' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:264:9: error: Common realloc mistake: 'in' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:169:13: warning: If memory allocation fails, then there is a possible null pointer dereference: b [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assignment 'b=malloc(sizeof(*b))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:169:13: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:173:13: warning: If memory allocation fails, then there is a possible null pointer dereference: b [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assignment 'b=malloc(sizeof(*b))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:173:13: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:173:32: warning: If memory allocation fails, then there is a possible null pointer dereference: b [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assignment 'b=malloc(sizeof(*b))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:173:32: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:175:13: warning: If memory allocation fails, then there is a possible null pointer dereference: b [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assignment 'b=malloc(sizeof(*b))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:175:13: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:176:13: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:176:13: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:177:13: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:177:13: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:177:32: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:177:32: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:178:13: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:167:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:167:24: note: Assignment 'bu=malloc(sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:178:13: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:179:13: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:167:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:167:24: note: Assignment 'bu=malloc(sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:179:13: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:207:45: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:207:45: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:207:59: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:207:59: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:213:36: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:213:36: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:17: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:17: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:51: warning: If memory allocation fails, then there is a possible null pointer dereference: b [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assignment 'b=malloc(sizeof(*b))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:51: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:61: warning: If memory allocation fails, then there is a possible null pointer dereference: b [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:166:23: note: Assignment 'b=malloc(sizeof(*b))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:61: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:70: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:214:70: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:215:31: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:215:31: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:216:17: warning: If memory allocation fails, then there is a possible null pointer dereference: bc [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:168:24: note: Assignment 'bc=malloc(sizeof(*bc))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:216:17: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:223:45: warning: If memory allocation fails, then there is a possible null pointer dereference: bu [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:167:24: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:167:24: note: Assignment 'bu=malloc(sizeof(*bu))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:223:45: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:317:29: style: Checking if unsigned expression 'in_size' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/htscodecs/tests/tokenise_name3_test.c:71:13: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/rANS_static4x16pr_test.c:156:39: style: Variable 'out_sz' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/tests/tokenise_name3_test.c:173:13: style: Variable 'argc' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/tests/tokenise_name3_test.c:174:13: style: Variable 'argv' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/tests/varint_test.c:279:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:444:64: style: Condition 'fqz_manual_parameters(gp,s,in2,in2_len)<0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:444:42: note: Calling function 'fqz_manual_parameters' returns 0 Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:444:64: note: Condition 'fqz_manual_parameters(gp,s,in2,in2_len)<0' is always false Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:244:13: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:65:54: warning: If memory allocation fails, then there is a possible null pointer dereference: len [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:431:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:431:30: note: Assignment 'rec_len=calloc(nlines,sizeof(*rec_len))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:442:48: note: Calling function 'fake_slice', 2nd argument 'rec_len' value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:65:54: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:65:66: warning: If memory allocation fails, then there is a possible null pointer dereference: len [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:431:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:431:30: note: Assignment 'rec_len=calloc(nlines,sizeof(*rec_len))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:442:48: note: Calling function 'fake_slice', 2nd argument 'rec_len' value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:65:66: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:74:30: warning: If memory allocation fails, then there is a possible null pointer dereference: len [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:431:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:431:30: note: Assignment 'rec_len=calloc(nlines,sizeof(*rec_len))', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:442:48: note: Calling function 'fake_slice', 2nd argument 'rec_len' value is 0 Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:74:30: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:387:29: style: Local variable 'out_len' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:321:20: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:387:29: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:64:44: style: Parameter 'len' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:64:54: style: Parameter 'r2' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:64:63: style: Parameter 'sel' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:223:34: style: Parameter 'fn' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:265:32: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:127:34: style: Variable 'st' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/tests/fqzcomp_qual_test.c:456:17: style: Variable 'in2' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/hts_expr.c:104:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization] Rhtslib/src/htslib-1.18/hts_expr.c:101:14: note: l is initialized Rhtslib/src/htslib-1.18/hts_expr.c:104:12: note: l is overwritten Rhtslib/src/htslib-1.18/hts_expr.c:121:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization] Rhtslib/src/htslib-1.18/hts_expr.c:118:14: note: l is initialized Rhtslib/src/htslib-1.18/hts_expr.c:121:12: note: l is overwritten Rhtslib/src/htslib-1.18/hts_expr.c:138:12: style: Redundant initialization for 'l'. The initialized value is overwritten before it is read. [redundantInitialization] Rhtslib/src/htslib-1.18/hts_expr.c:135:14: note: l is initialized Rhtslib/src/htslib-1.18/hts_expr.c:138:12: note: l is overwritten Rhtslib/src/htslib-1.18/hts_expr.c:48:9: style: struct member 'hts_filter_t::parsed' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/kstring.c:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/kstring.c:293:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/kstring.c:326:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/multipart.c:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/multipart.c:122:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/multipart.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/multipart.c:259:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/plugin.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/plugin.c:77:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUGIN_EXT [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/plugin.c:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/plugin.c:190:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/kstring.c:212:44: style:inconclusive: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/kstring.h:117:45: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'. Rhtslib/src/htslib-1.18/kstring.c:212:44: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'. Rhtslib/src/htslib-1.18/kstring.c:395:31: style: Variable 'bmBc' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/multipart.c:89:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] Rhtslib/src/htslib-1.18/multipart.c:90:68: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/multipart.c:140:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/multipart.c:114:39: note: Parameter 'fpv' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/multipart.c:140:38: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/multipart.c:120:36: note: Parameter 'fpv' can be declared as pointer to const Rhtslib/src/htslib-1.18/plugin.c:107:24: style: Variable 'e' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/md5.c:271:35: style:inconclusive: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:1487:39: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'. Rhtslib/src/htslib-1.18/md5.c:271:35: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:176:21: style: Condition '!rle' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:172:17: note: Assuming that condition 'rle' is not redundant Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:176:21: note: Condition '!rle' is always true Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:231:24: style: Condition 'cp>=cp_end' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:220:19: note: Assuming that condition 'cp>=cp_end' is not redundant Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:231:24: note: Condition 'cp>=cp_end' is always false Rhtslib/src/htslib-1.18/probaln.c:86:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:218:31: style: Same expression on both sides of '-'. [duplicateExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:226:50: style: Same expression on both sides of '-'. [duplicateExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:227:50: style: Same expression on both sides of '-'. [duplicateExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:231:21: style: Same expression on both sides of '-'. [duplicateExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:231:36: style: Same expression on both sides of '-'. [duplicateExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:231:50: style: Same expression on both sides of '-'. [duplicateExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:137:21: style: Local variable 'm' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:98:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:137:21: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:153:36: style: Local variable 's0' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:143:32: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:153:36: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:154:36: style: Local variable 's1' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:144:32: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:154:36: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:155:36: style: Local variable 's2' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:145:32: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:155:36: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:156:36: style: Local variable 's3' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:146:32: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:156:36: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:71:25: style: Variable 'out_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:143:32: style: Variable 's0' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:144:32: style: Variable 's1' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:145:32: style: Variable 's2' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:146:32: style: Variable 's3' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:153:36: style: Variable 's0' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:154:36: style: Variable 's1' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:155:36: style: Variable 's2' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:156:36: style: Variable 's3' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:191:26: style: Variable 'C' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:692:26: style: Variable 'S' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:704:26: style: Variable 'F' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static32x16pr.c:710:26: style: Variable 'B' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_word.h:105:44: style: Parameter 'r' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_word.h:137:46: style: Parameter 'r' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_word.h:468:77: style: Parameter 'ptr_end' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:165:58: style: Parameter 'F' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:166:14: style: Variable 'op' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:191:57: style: Parameter 'cp_end' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:195:14: style: Variable 'op' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:278:56: style: Parameter 'F0' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:278:70: style: Parameter 'F' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:279:14: style: Variable 'op' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:391:19: style: Variable 'F_i_' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:430:55: style: Parameter 'cp_end' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:430:73: style: Parameter 'F0' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:435:14: style: Variable 'op' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static16_int.h:545:42: style: Parameter 'F' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/samples/add_header.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/regidx.c:162:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/cram.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/cram.c:53:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/probaln.c:182:16: style: Variable 'E' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/probaln.c:305:16: style: Variable 'E' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/probaln.c:381:27: style: Variable 'fi' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/probaln.c:381:46: style: Variable 'bi' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/probaln.c:416:25: style: Variable 'sum' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/samples/dump_aux.c:126:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/flags_demo.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/dump_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/flags_demo.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/flags_htsopt_field.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/flags_htsopt_field.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/index_multireg_read.c:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/index_reg_read.c:68:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/index_multireg_read.c:117:12: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition] Rhtslib/src/htslib-1.18/samples/index_multireg_read.c:74:9: warning: If memory allocation fails, then there is a possible null pointer dereference: regions [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/samples/index_multireg_read.c:70:21: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/samples/index_multireg_read.c:70:21: note: Assignment 'regions=calloc(regcnt,sizeof(char*))', assigned value is 0 Rhtslib/src/htslib-1.18/samples/index_multireg_read.c:74:9: note: Null pointer dereference Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1145:23: style: Condition '*out_size==0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1144:45: note: Calling function 'rans_compress_bound_4x16' returns !<=1 Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1145:23: note: Condition '*out_size==0' is always false Rhtslib/src/htslib-1.18/samples/index_write.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/mod_aux.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/mod_aux_ba.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1530:18: style:inconclusive: Same expression used in consecutive assignments of 'tmp1_size' and 'tmp2_size'. [duplicateAssignExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1531:18: note: Same expression used in consecutive assignments of 'tmp1_size' and 'tmp2_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1530:18: note: Same expression used in consecutive assignments of 'tmp1_size' and 'tmp2_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1531:18: style:inconclusive: Same expression used in consecutive assignments of 'tmp2_size' and 'tmp3_size'. [duplicateAssignExpression] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1532:18: note: Same expression used in consecutive assignments of 'tmp2_size' and 'tmp3_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1531:18: note: Same expression used in consecutive assignments of 'tmp2_size' and 'tmp3_size'. Rhtslib/src/htslib-1.18/samples/mod_aux.c:115:27: portability:inconclusive: Casting from float * to const char * is not portable due to different binary data representations on different platforms. [invalidPointerCast] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:473:8: style: Redundant initialization for 'l3'. The initialized value is overwritten before it is read. [redundantInitialization] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:470:22: note: l3 is initialized Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:473:8: note: l3 is overwritten Rhtslib/src/htslib-1.18/samples/mod_aux_ba.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/region.c:43:21: style: Variable 'a' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/region.c:44:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/region.c:87:35: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:763:22: style: Local variable 'F0' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:587:14: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:763:22: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1218:17: style: Local variable 'j' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1175:16: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1218:17: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1592:22: style: Local variable 'osz' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1498:18: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1592:22: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1605:18: style: Local variable 'c_meta_size' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1529:14: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1605:18: note: Shadow variable Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1605:40: style: Local variable 'sz' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1497:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1605:40: note: Shadow variable Rhtslib/src/htslib-1.18/samples/modstate.c:64:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:114:25: style: Variable 'out_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:185:24: style: Variable 's3' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:186:24: style: Variable 's2' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:187:24: style: Variable 's1' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:188:24: style: Variable 's0' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:354:34: style: Parameter 'F0' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:354:68: style: Parameter 'T' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:482:24: style: Variable 's3' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:483:24: style: Variable 's2' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:484:24: style: Variable 's1' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:485:24: style: Variable 's0' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1151:20: style: Variable 'out_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1187:32: style: Variable 'ink' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1402:20: style: Variable 'in_end' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/samples/mod_bam.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/mpileup.c:96:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1300:21: style: Variable 'do_pack' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/rANS_static4x16pr.c:1341:20: style: Variable 'do_rle' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/mpileup.c:138:36: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/mpileup.c:56:26: note: Parameter 'data' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/mpileup.c:138:36: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/mpileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/mpileup.c:139:35: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/mpileup.c:60:25: note: Parameter 'data' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/mpileup.c:139:35: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/mpileup.c:60:63: note: Parameter 'cd' can be declared as pointer to const Rhtslib/src/htslib-1.18/samples/pileup.c:104:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/pileup_mod.c:109:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/pileup.c:131:34: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/pileup.c:56:26: note: Parameter 'data' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/pileup.c:131:34: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/pileup.c:56:64: note: Parameter 'cd' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/pileup.c:132:33: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/pileup.c:65:25: note: Parameter 'data' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/samples/pileup.c:132:33: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/samples/pileup.c:65:63: note: Parameter 'cd' can be declared as pointer to const Rhtslib/src/htslib-1.18/samples/modstate.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/modstate.c:56:77: style: Variable 'bm' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:247:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:252:17: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:254:17: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:269:13: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:292:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:294:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:295:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:296:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:297:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] Rhtslib/src/htslib-1.18/samples/read_aux.c:122:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/read_bam.c:63:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1498:13: error: Common realloc mistake: 'rev_a' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1499:13: error: Common realloc mistake: 'len_a' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1529:9: error: Common realloc mistake: 'rev_a' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1530:9: error: Common realloc mistake: 'len_a' nulled but not freed upon failure [memleakOnRealloc] Rhtslib/src/htslib-1.18/samples/read_fast.c:58:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1022:33: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1021:50: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1021:27: note: Assignment 'comp=(unsigned char*)malloc(in_size*1.1+100000)', assigned value is 0 Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1022:33: note: Null pointer addition Rhtslib/src/htslib-1.18/samples/read_fast.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/read_refname.c:55:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/read_bam.c:114:18: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/samples/read_bam.c:55:20: note: Shadowed declaration Rhtslib/src/htslib-1.18/samples/read_bam.c:114:18: note: Shadow variable Rhtslib/src/htslib-1.18/samples/read_bam.c:48:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/read_aux.c:114:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/rem_header.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/split.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/read_header.c:56:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/read_refname.c:91:13: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition] Rhtslib/src/htslib-1.18/samples/read_refname.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/split.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/rem_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/split2.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/split_thread1.c:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/split_thread2.c:62:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/split2.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1086:8: style: Variable 'pm' is reassigned a value before the old one has been used. [redundantAssignment] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1060:8: note: pm is assigned Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1086:8: note: pm is overwritten Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1183:14: style: Variable 'rec' is reassigned a value before the old one has been used. [redundantAssignment] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1157:9: note: rec is assigned Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1183:14: note: rec is overwritten Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1378:34: style: Checking if unsigned expression 'len' is less than zero. [unsignedLessThanZero] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1575:61: style:inconclusive: Function 'fqz_compress' argument 4 names different: declaration 'in_size' definition 'uncomp_size'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.h:152:61: note: Function 'fqz_compress' argument 4 names different: declaration 'in_size' definition 'uncomp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1575:61: note: Function 'fqz_compress' argument 4 names different: declaration 'in_size' definition 'uncomp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1576:28: style:inconclusive: Function 'fqz_compress' argument 5 names different: declaration 'out_size' definition 'comp_size'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.h:153:28: note: Function 'fqz_compress' argument 5 names different: declaration 'out_size' definition 'comp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1576:28: note: Function 'fqz_compress' argument 5 names different: declaration 'out_size' definition 'comp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1586:39: style:inconclusive: Function 'fqz_decompress' argument 2 names different: declaration 'in_size' definition 'comp_size'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.h:166:39: note: Function 'fqz_decompress' argument 2 names different: declaration 'in_size' definition 'comp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1586:39: note: Function 'fqz_decompress' argument 2 names different: declaration 'in_size' definition 'comp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1586:58: style:inconclusive: Function 'fqz_decompress' argument 3 names different: declaration 'out_size' definition 'uncomp_size'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.h:166:56: note: Function 'fqz_decompress' argument 3 names different: declaration 'out_size' definition 'uncomp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1586:58: note: Function 'fqz_decompress' argument 3 names different: declaration 'out_size' definition 'uncomp_size'. Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1114:13: style: Local variable 'j' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1015:15: note: Shadowed declaration Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1114:13: note: Shadow variable Rhtslib/src/htslib-1.18/samples/write_fast.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/samples/split_thread1.c:50:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/split_thread2.c:51:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/samples/update_header.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:212:5: warning:inconclusive: Found suspicious operator '*', result is not used. [constStatement] Rhtslib/src/htslib-1.18/samples/write_fast.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:102:58: style: Parameter 'array' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:146:38: style: Parameter 'in' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:229:38: style: Parameter 'tab' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:229:59: style: Parameter 'name' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:264:36: style: Parameter 'map' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:264:57: style: Parameter 'name' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:320:57: style: Parameter 'gp' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:933:41: style: Parameter 'pm' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1022:20: style: Variable 'compe' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1346:43: style: Parameter 'pm' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1350:63: style: Parameter 'out_size' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/samples/update_header.c:49:26: style: Parameter 'argv' can be declared as const array [constParameter] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:690:20: style: Variable 'j' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/fqzcomp_qual.c:1159:21: style: Variable 'j' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/test/hfile.c:40:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hfile.c:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hfile.c:107:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hts_endian.c:169:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hts_endian.c:252:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hts_endian.c:333:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hts_endian.c:415:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hts_endian.c:460:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hts_endian.c:508:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/regidx.c:438:68: style: Condition 'list->reg[ireg].beg<=end' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/regidx.c:437:38: note: Assuming that condition 'list->reg[ireg].beg>end' is not redundant Rhtslib/src/htslib-1.18/regidx.c:438:68: note: Condition 'list->reg[ireg].beg<=end' is always true Rhtslib/src/htslib-1.18/regidx.c:629:63: style: Condition 'list->reg[i].beg<=itr->end' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/regidx.c:628:31: note: Assuming that condition 'list->reg[i].beg>itr->end' is not redundant Rhtslib/src/htslib-1.18/regidx.c:629:63: note: Condition 'list->reg[i].beg<=itr->end' is always true Rhtslib/src/htslib-1.18/regidx.c:207:42: style:inconclusive: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:150:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. Rhtslib/src/htslib-1.18/regidx.c:207:42: note: Function 'regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. Rhtslib/src/htslib-1.18/regidx.c:207:119: style:inconclusive: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:150:121: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. Rhtslib/src/htslib-1.18/regidx.c:207:119: note: Function 'regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. Rhtslib/src/htslib-1.18/regidx.c:244:114: style:inconclusive: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:148:113: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. Rhtslib/src/htslib-1.18/regidx.c:244:114: note: Function 'regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. Rhtslib/src/htslib-1.18/regidx.c:399:30: style:inconclusive: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:167:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. Rhtslib/src/htslib-1.18/regidx.c:399:30: note: Function 'regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. Rhtslib/src/htslib-1.18/regidx.c:399:95: style:inconclusive: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:167:92: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:399:95: note: Function 'regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:582:33: style:inconclusive: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:212:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. Rhtslib/src/htslib-1.18/regidx.c:582:33: note: Function 'regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. Rhtslib/src/htslib-1.18/regidx.c:597:29: style:inconclusive: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:216:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. Rhtslib/src/htslib-1.18/regidx.c:597:29: note: Function 'regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. Rhtslib/src/htslib-1.18/regidx.c:597:47: style:inconclusive: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:216:44: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:597:47: note: Function 'regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:604:31: style:inconclusive: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:214:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:604:31: note: Function 'regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:610:30: style:inconclusive: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:223:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:610:30: note: Function 'regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:644:27: style:inconclusive: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/regidx.h:230:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/regidx.c:644:27: note: Function 'regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. Rhtslib/src/htslib-1.18/tbx.c:439:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/regidx.c:105:35: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/regidx.c:132:35: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/regidx.c:132:45: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/regidx.c:149:38: style: Parameter 'chr_beg' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/regidx.c:149:53: style: Parameter 'chr_end' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/regidx.c:149:98: style: Parameter 'payload' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/regidx.c:682:13: style: Variable 'src_itr' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/regidx.c:48:15: style: struct member 'pos_t::pos' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/regidx.c:49:15: style: struct member 'pos_t::ireg' is never used. [unusedStructMember] Rhtslib/src/htslib-1.18/test/test-bcf-sr.c:47:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-bcf-sr.c:54:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-bcf-sr.c:145:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/hts_endian.c:149:31: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/test/test-bcf-translate.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-bcf-translate.c:114:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-regidx.c:50:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-regidx.c:60:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-regidx.c:69:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-regidx.c:193:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-regidx.c:417:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-regidx.c:441:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-bcf-sr.c:75:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/test/test-bcf-sr.c:92:21: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/test/test-bcf-sr.c:125:26: style: Variable 'loptions' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:86:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:126:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pair [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:201:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:220:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable targets_overlap [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:412:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:447:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:455:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:668:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable regions_overlap [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:761:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:859:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sort [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:989:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1433:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:40:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:52:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:112:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:288:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:407:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:435:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:493:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:547:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:586:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-vcf-sweep.c:35:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_expr.c:307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test-regidx.c:92:11: style: Variable 'se' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/test/test-regidx.c:250:11: style: Variable 'beg' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/test/test-regidx.c:457:10: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/test/test-regidx.c:307:53: note: Parameter 'chr' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/test/test-regidx.c:451:10: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/test/test-regidx.c:311:53: note: Parameter 'chr' can be declared as pointer to const Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/test/test-regidx.c:454:10: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/test/test-regidx.c:315:53: note: Parameter 'chr' can be declared as pointer to const Rhtslib/src/htslib-1.18/test/test-regidx.c:428:26: style: Variable 'loptions' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/test/test_bgzf.c:71:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:81:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:93:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:113:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:125:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:147:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:168:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:184:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:194:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:207:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:218:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:228:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:238:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:248:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:258:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:270:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:281:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:291:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:302:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:318:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:332:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:367:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:408:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:444:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:524:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:590:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:623:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:646:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:741:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:842:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:888:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:949:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:1035:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_expr.c:101:19: warning: Either the condition 'a' is redundant or there is possible null pointer dereference: a. [nullPointerRedundantCheck] Rhtslib/src/htslib-1.18/test/test_expr.c:100:9: note: Assuming that condition 'a' is not redundant Rhtslib/src/htslib-1.18/test/test_expr.c:101:19: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test_faidx.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:91:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:104:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:275:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:300:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:325:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:355:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:382:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_faidx.c:445:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/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] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:203:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:34: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 Rhtslib/src/htslib-1.18/test/test-vcf-api.c:203:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test-vcf-api.c:204:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:34: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 Rhtslib/src/htslib-1.18/test/test-vcf-api.c:204:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test-vcf-api.c:205:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:34: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 Rhtslib/src/htslib-1.18/test/test-vcf-api.c:205:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test-vcf-api.c:206:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:34: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 Rhtslib/src/htslib-1.18/test/test-vcf-api.c:206:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test-vcf-api.c:207:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:34: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 Rhtslib/src/htslib-1.18/test/test-vcf-api.c:207:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test-vcf-api.c:208:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:34: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/test-vcf-api.c:202:22: note: Assignment 'tmpia=(int*)malloc(hdr->n[2]*2*sizeof(int))', assigned value is 0 Rhtslib/src/htslib-1.18/test/test-vcf-api.c:208:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test-vcf-api.c:254:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpfa [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:253:34: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/test-vcf-api.c:253:20: note: Assignment 'tmpfa=(float*)malloc(2*sizeof(float))', assigned value is 0 Rhtslib/src/htslib-1.18/test/test-vcf-api.c:254:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/test/test-vcf-api.c:69:44: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/test/test-vcf-api.c:357:17: style: Variable 'tmpia' can be declared as const array [constVariable] Rhtslib/src/htslib-1.18/tbx.c:248:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/tbx.c:248:18: note: Calling function 'ed_is_big' returns 0 Rhtslib/src/htslib-1.18/tbx.c:248:18: note: Condition 'ed_is_big()' is always false Rhtslib/src/htslib-1.18/test/test_kfunc.c:43:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kfunc.c:84:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/tbx.c:253:13: style: Local variable 'x' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/tbx.c:231:14: note: Shadowed declaration Rhtslib/src/htslib-1.18/tbx.c:253:13: note: Shadow variable Rhtslib/src/htslib-1.18/tbx.c:76:19: style: Variable 'ss_dup' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/tbx.c:410:11: style: Variable 'nm' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/test/test_kstring.c:51:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kstring.c:102:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kstring.c:134:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kstring.c:200:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kstring.c:314:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kstring.c:370:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kstring.c:392:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_bgzf.c:518:56: warning: Either the condition 'pos Rhtslib/src/htslib-1.18/htscodecs/htscodecs/tokenise_name3.c:1347:19: note: Assuming condition is false Rhtslib/src/htslib-1.18/htscodecs/htscodecs/tokenise_name3.c:1384:21: note: Uninitialized variable: best_dat Rhtslib/src/htslib-1.18/test/thrash_threads6.c:94:17: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] Rhtslib/src/htslib-1.18/htscodecs/htscodecs/tokenise_name3.c:820:19: style: Variable 'd' is assigned a value that is never used. [unreadVariable] Rhtslib/src/htslib-1.18/test/thrash_threads7.c:45:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] Rhtslib/src/htslib-1.18/test/thrash_threads7.c:44:19: style: Variable 'usecs' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/thread_pool.c:752:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_RECURSIVE [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/thread_pool.c:856:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/test/test_kstring.c:50:13: style: Condition 'val!=0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/test/test_kstring.c:45:11: note: Assignment 'val=0', assigned value is 0 Rhtslib/src/htslib-1.18/test/test_kstring.c:50:13: note: Condition 'val!=0' is always false Rhtslib/src/htslib-1.18/test/test_kstring.c:380:11: style: Variable 'test' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcf_sweep.c:82:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/vcf_sweep.c:106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/vcf_sweep.c:174:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:411:5: warning: If memory allocation fails, then there is a possible null pointer dereference: files [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:410:43: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:410:24: note: Assignment 'files=(struct bcf_srs_t*)calloc(1,sizeof(struct bcf_srs_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:411:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:412:23: warning: If memory allocation fails, then there is a possible null pointer dereference: files [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:410:43: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:410:24: note: Assignment 'files=(struct bcf_srs_t*)calloc(1,sizeof(struct bcf_srs_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:412:23: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1041:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:56: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:29: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1041:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1041:18: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:56: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:29: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1041:18: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1042:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:56: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:29: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1042:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1042:23: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:56: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:29: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1042:23: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1042:39: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:56: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1040:29: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1042:39: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1193:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:38: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:11: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1193:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1193:18: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:38: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:11: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1193:18: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1194:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:38: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:11: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1194:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1194:23: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:38: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:11: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1194:23: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1194:39: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:38: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:11: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1194:39: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1196:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:38: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:11: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1196:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1197:11: warning: If memory allocation fails, then there is a possible null pointer dereference: reg [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:38: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1192:11: note: Assignment 'reg=(struct bcf_sr_regions_t*)calloc(1,sizeof(struct bcf_sr_regions_t))', assigned value is 0 Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1197:11: note: Null pointer dereference Rhtslib/src/htslib-1.18/synced_bcf_reader.c:249:34: style:inconclusive: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:237:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:249:34: note: Function 'bcf_sr_add_reader' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:434:32: style:inconclusive: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:204:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:434:32: note: Function 'bcf_sr_destroy' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:814:33: style:inconclusive: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:251:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:814:33: note: Function 'bcf_sr_next_line' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:885:35: style:inconclusive: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:281:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:885:35: note: Function 'bcf_sr_set_samples' argument 1 names different: declaration 'readers' definition 'files'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:885:54: style:inconclusive: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:281:56: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:885:54: note: Function 'bcf_sr_set_samples' argument 2 names different: declaration 'samples' definition 'fname'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1182:77: style:inconclusive: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:348:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1182:77: note: Function 'bcf_sr_regions_init' argument 3 names different: declaration 'chr' definition 'ichr'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1182:87: style:inconclusive: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:348:86: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1182:87: note: Function 'bcf_sr_regions_init' argument 4 names different: declaration 'from' definition 'ifrom'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1182:98: style:inconclusive: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:348:96: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1182:98: note: Function 'bcf_sr_regions_init' argument 5 names different: declaration 'to' definition 'ito'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1262:47: style:inconclusive: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:351:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1262:47: note: Function 'bcf_sr_regions_destroy' argument 1 names different: declaration 'regions' definition 'reg'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1287:43: style:inconclusive: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:360:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1287:43: note: Function 'bcf_sr_regions_seek' argument 1 names different: declaration 'regions' definition 'reg'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1287:60: style:inconclusive: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:360:64: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1287:60: note: Function 'bcf_sr_regions_seek' argument 2 names different: declaration 'chr' definition 'seq'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1494:44: style:inconclusive: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/synced_bcf_reader.h:390:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1494:44: note: Function 'bcf_sr_regions_flush' argument 1 names different: declaration 'regs' definition 'reg'. Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1456:33: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:147:37: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:385:20: style: Variable 'hdr0' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:386:20: style: Variable 'hdr1' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:491:40: style: Parameter 'reader' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:491:56: style: Parameter 'line' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:584:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:585:19: style: Variable 'alt' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:999:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1000:16: style: Variable 'b' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/synced_bcf_reader.c:1332:20: style: Variable 'creg' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/thread_pool.c:1048:36: style: Condition 'hts_tpool_process_flush(q)!=0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/thread_pool.c:1048:32: note: Calling function 'hts_tpool_process_flush' returns 0 Rhtslib/src/htslib-1.18/thread_pool.c:1048:36: note: Condition 'hts_tpool_process_flush(q)!=0' is always false Rhtslib/src/htslib-1.18/thread_pool.c:354:47: style: Parameter 'r' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/thread_pool.c:473:43: style: Variable 'first' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/thread_pool.c:815:31: style: Parameter 'p' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/thread_pool.c:1077:48: style: Parameter 'q' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/vcf_sweep.c:117:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:117:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:118:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:118:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:118:30: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:118:30: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:119:9: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:119:9: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:120:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:120:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:120:29: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:120:29: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:121:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:121:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:122:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:122:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:122:33: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:122:33: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:123:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:123:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:124:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/vcf_sweep.c:116:44: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/vcf_sweep.c:116:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0 Rhtslib/src/htslib-1.18/vcf_sweep.c:124:5: note: Null pointer dereference Rhtslib/src/htslib-1.18/vcf_sweep.c:58:45: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/vcf_sweep.c:64:11: style: Variable 't' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcf_sweep.c:189:39: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer] Rhtslib/src/htslib-1.18/vcfutils.c:61:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/vcfutils.c:216:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/vcfutils.c:303:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable info [valueFlowBailoutIncompleteVar] Rhtslib/src/htslib-1.18/vcfutils.c:463:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] Rhtslib/src/htslib-1.18/vcfutils.c:497:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] Rhtslib/src/htslib-1.18/vcfutils.c:775:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] Rhtslib/src/htslib-1.18/vcfutils.c:829:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] Rhtslib/src/htslib-1.18/vcfutils.c:134:55: style:inconclusive: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcfutils.h:117:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. Rhtslib/src/htslib-1.18/vcfutils.c:134:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. Rhtslib/src/htslib-1.18/vcfutils.c:134:66: style:inconclusive: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcfutils.h:117:65: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. Rhtslib/src/htslib-1.18/vcfutils.c:134:66: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. Rhtslib/src/htslib-1.18/vcfutils.c:241:67: style:inconclusive: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcfutils.h:61:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. Rhtslib/src/htslib-1.18/vcfutils.c:241:67: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. Rhtslib/src/htslib-1.18/vcfutils.c:43:13: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/vcfutils.c:34:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcfutils.c:43:13: note: Shadow variable Rhtslib/src/htslib-1.18/vcfutils.c:96:13: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/vcfutils.c:34:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcfutils.c:96:13: note: Shadow variable Rhtslib/src/htslib-1.18/vcfutils.c:579:17: style: Local variable 'size' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/vcfutils.c:563:13: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcfutils.c:579:17: note: Shadow variable Rhtslib/src/htslib-1.18/vcfutils.c:44:18: style: Variable 'ac_ptr' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:462:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:463:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:496:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:497:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:624:56: style: Variable 'se' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:774:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:775:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:828:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] Rhtslib/src/htslib-1.18/vcfutils.c:829:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer] diff: 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1000:29: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1039:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1000:29: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1004:65: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3977:20: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1004:65: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1027:48: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3856:5: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1027:48: note: Parameter 'st' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1051:93: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4059:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1051:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1069:92: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4057:26: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1069:92: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1087:93: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4061:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1087:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1163:34: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4056:20: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1163:34: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1188:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1200:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1212:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1301:94: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4072:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1301:94: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1316:93: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4074:30: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1316:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1365:94: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4076:30: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1365:94: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1430:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1495:35: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4071:19: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1495:35: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1540:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1551:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1561:34: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4077:24: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1561:34: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1615:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1635:60: error: Shifting signed 32-bit value by 31 bits is undefined behaviour [shiftTooManyBitsSigned] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:41: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1752:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:41: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:60: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1752:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:75: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1752:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:75: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:85: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1752:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:85: note: Parameter 'out' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:95: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1752:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1641:95: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1645:94: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1754:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1645:94: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1662:55: style: Parameter 'slice' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1662:74: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:41: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1756:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:41: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:60: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1756:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:75: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1756:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:75: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:85: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1756:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:85: note: Parameter 'out' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:95: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1756:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1666:95: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1677:47: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1759:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1677:47: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1708:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1784:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1847:19: style: Variable 'dat' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1860:18: style: Variable 'dat' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1888:35: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1997:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1888:35: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1923:41: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1992:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1923:41: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1923:60: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1992:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1923:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1924:34: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1992:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1924:34: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1928:40: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1994:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1928:40: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1928:59: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1994:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1928:59: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1929:33: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1994:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1929:33: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1951:19: style: Variable 'in16' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:39: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2155:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:39: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:58: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2155:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:58: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:73: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2155:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:73: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:83: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2155:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:83: note: Parameter 'out' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:93: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2155:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2020:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:38: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2157:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:38: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:57: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2157:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:57: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:72: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2157:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:72: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:82: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2157:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:82: note: Parameter 'out' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:92: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2157:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2025:92: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2082:93: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2159:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2082:93: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2093:5: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2161:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2260:35: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2383:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2260:35: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2315:39: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2378:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2315:39: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2315:58: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2378:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2315:58: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2316:34: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2378:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2316:34: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2321:38: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2380:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2321:38: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2321:57: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2380:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2321:57: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2322:33: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2380:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2322:33: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2408:90: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2481:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2408:90: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2502:89: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2556:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2502:89: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2597:42: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2839:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2597:42: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2597:61: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2839:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2597:61: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2598:42: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2839:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2598:42: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2598:52: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2839:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2598:52: note: Parameter 'out' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2598:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2839:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2598:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2603:63: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4032:26: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2603:63: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2617:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4034:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2617:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2652:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4036:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2652:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2665:61: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4038:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2665:61: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2702:63: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4040:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2702:63: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2715:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4042:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2715:62: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2794:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2921:62: style: Condition 'option==E_BYTE' is always false [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2940:43: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4033:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2940:43: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2940:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4033:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2940:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2941:37: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4033:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2941:37: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2948:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2952:17: style: Condition 'sym>=-1' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2951:19: note: Assignment 'sym=*syms++', assigned value is greater than -1 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2952:17: note: Condition 'sym>=-1' is always true 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2976:42: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4037:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2976:42: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2976:61: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4037:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2976:61: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2977:36: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4037:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2977:36: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:2984:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3013:43: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4041:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3013:43: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3013:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4041:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3013:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3014:37: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4041:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3014:37: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3021:14: style: Variable 'syms' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3063:67: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4022:20: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3063:67: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3077:33: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3076:23: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3076:23: note: Assignment 'tmp=malloc(6*c->u.e_huffman.nvals+16)', assigned value is 0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3077:33: note: Null pointer addition 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3165:17: style: Local variable 'k' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3134:44: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3165:17: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3453:44: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4093:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3453:44: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3532:76: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3642:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3532:76: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3535:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3573:25: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3592:24: style: Variable 'cp_start' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3673:39: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4114:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3673:39: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3689:45: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4113:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3689:45: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:386:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3988:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:386:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:389:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:406:70: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3990:31: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:406:70: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:409:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:435:62: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:500:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:435:62: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:436:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:446:68: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:501:20: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:446:68: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:544:37: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3991:25: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:544:37: note: Parameter 'in' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:558:68: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3983:20: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:558:68: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:585:45: style: Parameter 'dat' can be declared as pointer to const. However it seems that 'cram_external_encode_init' is a callback function, if 'dat' is declared with const you might also need to cast function pointer(s). [constParameterCallback] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3837:5: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:585:45: note: Parameter 'dat' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:733:60: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:789:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:733:60: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:734:17: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:744:66: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:790:20: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:744:66: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:797:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:809:15: style: Variable 'i32' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:816:14: style: Variable 'i32' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:823:15: style: Variable 'i64' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:830:14: style: Variable 'i64' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:841:66: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:4000:20: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:841:66: note: Parameter 'prefix' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:865:49: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3854:5: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:865:49: note: Parameter 'st' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:868:43: style: Parameter 'dat' can be declared as pointer to const. However it seems that 'cram_varint_encode_init' is a callback function, if 'dat' is declared with const you might also need to cast function pointer(s). [constParameterCallback] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:3854:5: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:868:43: note: Parameter 'dat' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:920:60: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:978:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:920:60: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:930:59: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:980:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:930:59: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:941:60: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:982:21: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:941:60: note: Parameter 'out_size' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:956:40: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:984:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:956:40: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:956:59: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:984:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:956:59: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:991:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:999:35: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1039:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:999:35: note: Parameter 'slice' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.c:999:54: 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] Rhtslib/src/htslib-1.18/cram/cram_codecs.c:1039:17: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/cram/cram_codecs.c:999:54: note: Parameter 'c' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_codecs.h:230:52: style: Parameter 'blk' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1003:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1229:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1419:34: style: Variable 'dlen' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1505:38: style: Local variable 'r' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_decode.c:1099:26: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_decode.c:1505:38: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1512:29: style: Variable 'md_dist' is reassigned a value before the old one has been used. [redundantAssignment] Rhtslib/src/htslib-1.18/cram/cram_decode.c:1499:37: note: md_dist is assigned Rhtslib/src/htslib-1.18/cram/cram_decode.c:1512:29: note: md_dist is overwritten 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1708:31: style: Variable 'N' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1713:35: style: Variable 'refp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:175:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1814:28: style: Variable 'orig_aux_p' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1888:58: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1916:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_decode.c:1903:19: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_decode.c:1916:21: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1985:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_decode.c:1957:19: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_decode.c:1985:21: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1990:66: warning: Expression 'TN[2]=='*'?-1:1' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:1992:66: warning: Expression 'TN[2]=='*'?-1:1' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2233:39: style: Parameter 'md5' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2250:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2275:34: style:inconclusive: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/cram/cram_decode.h:105:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. Rhtslib/src/htslib-1.18/cram/cram_decode.c:2275:34: note: Function 'cram_decode_slice' argument 4 names different: declaration 'hdr' definition 'sh'. 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2286:18: style: Variable 'bfd' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2306:19: style: The if condition is the same as the previous if condition [duplicateCondition] Rhtslib/src/htslib-1.18/cram/cram_decode.c:2305:19: note: First condition Rhtslib/src/htslib-1.18/cram/cram_decode.c:2306:19: note: Second condition 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2435:25: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2869:31: style: Local variable 'c' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/cram/cram_decode.c:2274:52: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_decode.c:2869:31: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:2972:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:3007:48: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:3013:11: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:3013:17: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:552:41: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:875:55: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:881:21: style: Local variable 'c' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/cram/cram_decode.c:875:72: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_decode.c:881:21: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:926:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_decode.c:938:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1244:14: style: Variable 'TC' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:125:13: style: Local variable 'r' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:88:16: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:125:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1280:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1341:20: style: Variable 'b' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1373:36: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1417:29: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1417:58: style: Parameter 'skip' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1480:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1579:13: style: Local variable 'ret' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:1576:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:1579:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1587:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1591:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1604:28: style: Variable 'L16' can be declared as const array [constVariable] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1611:25: style: The comparison 'ret < 0' is always false. [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/cram/cram_encode.c:1576:15: note: 'ret' is assigned value '0' here. Rhtslib/src/htslib-1.18/cram/cram_encode.c:1611:25: note: The comparison 'ret < 0' is always false. 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1717:21: style: Variable 'm5tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1722:11: style: Variable 'ref' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:1783:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:2438:59: style: Parameter 'f' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:2493:51: style: Parameter 'base' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:2547:54: style: Parameter 'base' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:2651:58: style: Parameter 'MD' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:2658:11: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:2738:13: style: Local variable 'key' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:2658:11: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:2738:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:2773:25: style: Local variable 'c' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/cram/cram_encode.c:2648:55: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:2773:25: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3092:27: 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] Rhtslib/src/htslib-1.18/cram/cram_encode.c:3093:28: note: Assignment 'c->ref_seq_id=s->hdr->ref_seq_id' Rhtslib/src/htslib-1.18/cram/cram_encode.c:3092:27: note: Condition 'c->ref_seq_id!=s->hdr->ref_seq_id' is redundant 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3324:27: style: Variable 'sp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3325:27: style: Variable 'rp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3326:27: style: Variable 'qp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3548:20: style: Variable 'brg' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3558:24: style: Local variable 'brg' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:3548:20: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:3558:24: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3558:24: style: Variable 'brg' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3582:19: style: Variable 'from' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3589:25: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:3203:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:3589:25: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3591:39: style: Local variable 'c' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/cram/cram_encode.c:3199:58: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:3591:39: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3617:19: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:3958:25: style: Condition 'c->refs_used' is always true [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:567:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:653:22: style: Local variable 'i32' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:573:13: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:653:22: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:70:26: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:797:61: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:822:11: style: The if condition is the same as the previous if condition [duplicateCondition] Rhtslib/src/htslib-1.18/cram/cram_encode.c:812:11: note: First condition Rhtslib/src/htslib-1.18/cram/cram_encode.c:822:11: note: Second condition 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:845:13: style: Variable 'methodF' is reassigned a value before the old one has been used. [redundantAssignment] Rhtslib/src/htslib-1.18/cram/cram_encode.c:837:17: note: methodF is assigned Rhtslib/src/htslib-1.18/cram/cram_encode.c:845:13: note: methodF is overwritten 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:949:13: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:798:28: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:949:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_encode.c:967:13: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_encode.c:798:28: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_encode.c:967:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:104:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:120:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:490:61: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:494:59: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:498:54: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:515:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:516:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:517:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:518:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:519:41: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:520:58: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:523:64: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:544:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:558:50: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:58:40: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:61:34: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:64:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:65:30: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:67:32: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:739:49: style: Parameter 'out_rg' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:75:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:779:8: style: Redundant initialization for 'op'. The initialized value is overwritten before it is read. [redundantInitialization] Rhtslib/src/htslib-1.18/cram/cram_external.c:770:14: note: op is initialized Rhtslib/src/htslib-1.18/cram/cram_external.c:779:8: note: op is overwritten 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:84:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:92:56: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_external.c:96:54: style: Parameter 'c' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_index.c:405:42: style:inconclusive: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/cram/cram_index.h:54:81: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. Rhtslib/src/htslib-1.18/cram/cram_index.c:405:42: note: Function 'cram_index_query' argument 4 names different: declaration 'frm' definition 'from'. 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_index.c:474:30: style: Condition 'from->e[k].starte[k].start>=pos' is not redundant Rhtslib/src/htslib-1.18/cram/cram_index.c:474:30: note: Condition 'from->e[k].startcram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment] Rhtslib/src/htslib-1.18/cram/cram_io.c:5174:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned Rhtslib/src/htslib-1.18/cram/cram_io.c:5175:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5176:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment] Rhtslib/src/htslib-1.18/cram/cram_io.c:5175:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned Rhtslib/src/htslib-1.18/cram/cram_io.c:5176:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5177:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment] Rhtslib/src/htslib-1.18/cram/cram_io.c:5176:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned Rhtslib/src/htslib-1.18/cram/cram_io.c:5177:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5226:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5539:13: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_io.c:5498:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_io.c:5539:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5604:23: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5638:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5744:21: style: Variable 'r' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.c:5939:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_io.h:642:49: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_stats.c:167:13: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/cram/cram_stats.c:135:16: note: Shadowed declaration Rhtslib/src/htslib-1.18/cram/cram_stats.c:167:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/cram/cram_structs.h:67:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1070:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1104:40: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1177:22: style: Variable 'first' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1207:34: style:inconclusive: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:445:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1207:34: note: Function 'sam_hdr_length' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1209:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1214:36: style:inconclusive: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:458:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1214:36: note: Function 'sam_hdr_str' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1221:35: style:inconclusive: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:465:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1221:35: note: Function 'sam_hdr_nref' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1286:34: style:inconclusive: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:483:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1286:34: note: Function 'sam_hdr_add_lines' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1321:33: style:inconclusive: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:499:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1321:33: note: Function 'sam_hdr_add_line' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1335:47: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1354:37: style:inconclusive: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:518:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1354:37: note: Function 'sam_hdr_find_line_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1366:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1378:38: style:inconclusive: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:536:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1378:38: note: Function 'sam_hdr_find_line_pos' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1390:22: style: Variable 'ty' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1412:39: style:inconclusive: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:561:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1412:39: note: Function 'sam_hdr_remove_line_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:143:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1451:40: style:inconclusive: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:573:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1451:40: note: Function 'sam_hdr_remove_line_pos' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1500:11: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1500:17: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1502:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1538:36: style:inconclusive: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:600:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1538:36: note: Function 'sam_hdr_update_line' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1612:38: style:inconclusive: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:617:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1612:38: note: Function 'sam_hdr_remove_except' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1658:37: style:inconclusive: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:657:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1658:37: note: Function 'sam_hdr_remove_lines' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1658:81: style:inconclusive: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:657:80: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. Rhtslib/src/htslib-1.18/header.c:1658:81: note: Function 'sam_hdr_remove_lines' argument 4 names different: declaration 'rh' definition 'vrh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1660:15: style: Variable 'rh' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1688:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1704:22: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1709:17: style: Variable 'head' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1720:36: style:inconclusive: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:666:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1720:36: note: Function 'sam_hdr_count_lines' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1722:33: style: Variable 'itr_ty' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1860:36: style:inconclusive: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:707:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1860:36: note: Function 'sam_hdr_find_tag_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1880:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1885:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1892:37: style:inconclusive: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:725:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1892:37: note: Function 'sam_hdr_find_tag_pos' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1911:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1916:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/header.c:191:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/header.c:1923:38: style:inconclusive: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:736:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1923:38: note: Function 'sam_hdr_remove_tag_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:1970:33: style:inconclusive: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:749:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:1970:33: note: Function 'sam_hdr_name2tid' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:2128:38: style:inconclusive: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:792:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:2128:38: note: Function 'sam_hdr_pg_id' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:2179:31: style:inconclusive: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:810:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:2179:31: note: Function 'sam_hdr_add_pg' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:2250:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/header.c:2266:65: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/header.c:2283:34: style:inconclusive: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:830:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/header.c:2283:34: note: Function 'sam_hdr_incr_ref' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/header.c:2435:27: style: Variable 't2' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:2477:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:2510:15: style: Variable 'k' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:2510:19: style: Variable 'v' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:2608:25: style: Variable 'sn_tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:2728:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:311:25: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:404:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:41:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 Rhtslib/src/htslib-1.18/header.c:587:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:587:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:624:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:624:21: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:66:64: style: Parameter 'type_list' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:672:43: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/header.c:701:14: style: Variable 'hrecs->first_line' is assigned an expression that holds the same value. [redundantAssignment] Rhtslib/src/htslib-1.18/header.c:700:27: note: Assuming that condition 'hrecs->first_line==type_found' is not redundant Rhtslib/src/htslib-1.18/header.c:700:27: note: Assuming that condition 'hrecs->first_line==type_found' is not redundant Rhtslib/src/htslib-1.18/header.c:701:14: note: Variable 'hrecs->first_line' is assigned an expression that holds the same value. 2.19.0 Rhtslib/src/htslib-1.18/header.c:731:21: style: Variable 'tag' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/header.c:733:10: style: Variable 'c' can be declared as const array [constVariable] 2.19.0 Rhtslib/src/htslib-1.18/header.c:735:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/header.c:767:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SSIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1122:46: style: Same expression on both sides of '||'. [duplicateExpression] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1123:41: style: Condition 'strcmp(o->arg,"store_md")==0' is always false [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1126:46: style: Same expression on both sides of '||'. [duplicateExpression] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1127:41: style: Condition 'strcmp(o->arg,"store_nm")==0' is always false [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1191:14: style: Variable 'last' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1241:35: style:inconclusive: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:452:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. Rhtslib/src/htslib-1.18/hts.c:1241:35: note: Function 'hts_parse_opt_list' argument 1 names different: declaration 'opt' definition 'fmt'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1247:21: style: Redundant condition: The condition '*str' is redundant since '*str == ','' is sufficient. [redundantCondition] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1278:33: style:inconclusive: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:438:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. Rhtslib/src/htslib-1.18/hts.c:1278:33: note: Function 'hts_parse_format' argument 1 names different: declaration 'opt' definition 'format'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:136:43: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:138:38: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1391:48: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1404:27: style:inconclusive: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:629:34: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. Rhtslib/src/htslib-1.18/hts.c:1404:27: note: Function 'hts_hopen' argument 1 names different: declaration 'fp' definition 'hfile'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1408:34: style: Variable 'opts' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:140:39: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:142:46: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1438:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:144:41: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:146:40: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:152:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_CC [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1601:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1778:15: style: Variable 'expr' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1894:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1936:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1953:33: style:inconclusive: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:696:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. Rhtslib/src/htslib-1.18/hts.c:1953:33: note: Function 'hts_readlist' argument 1 names different: declaration 'fn' definition 'string'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:1968:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2027:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2117:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2118:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2382:36: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2398:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2427:64: style: Condition 'tid<0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/hts.c:2427:52: note: Assuming that condition 'idx->z.last_tid>=0' is not redundant Rhtslib/src/htslib-1.18/hts.c:2427:25: note: Assuming that condition 'idx->z.last_tid!=tid' is not redundant Rhtslib/src/htslib-1.18/hts.c:2427:64: note: Condition 'tid<0' is always false 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2558:28: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2567:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/hts.c:2567:18: note: Calling function 'ed_is_big' returns 0 Rhtslib/src/htslib-1.18/hts.c:2567:18: note: Condition 'ed_is_big()' is always false 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2573:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/hts.c:2573:18: note: Calling function 'ed_is_big' returns 0 Rhtslib/src/htslib-1.18/hts.c:2573:18: note: Condition 'ed_is_big()' is always false 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2579:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/htslib/hts.h:1543:15: note: Assignment 'one=1', assigned value is 1 Rhtslib/src/htslib-1.18/hts.c:2579:18: note: Calling function 'ed_is_big' returns 0 Rhtslib/src/htslib-1.18/hts.c:2579:18: note: Condition 'ed_is_big()' is always false 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2616:17: style: Variable 'lidx' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2624:29: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2656:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2738:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2746:17: style: Local variable 'j' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/hts.c:2717:13: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:2746:17: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2751:22: style: Condition 'l->n<0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/hts.c:2750:20: note: Assignment 'l->n=x', assigned value is greater than -1 Rhtslib/src/htslib-1.18/hts.c:2751:22: note: Condition 'l->n<0' is always false 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2789:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2851:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2867:38: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2885:17: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2930:112: style: Parameter 'bidx' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:2988:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3078:21: style: Local variable 'bin' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/hts.c:3071:19: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:3078:21: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3092:13: style: Variable 'bidx' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3145:20: style: Variable 'reg1' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3146:20: style: Variable 'reg2' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3217:23: style: Variable 'unmapped' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3222:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3229:22: style: Local variable 'off' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/hts.c:3212:23: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:3229:22: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3431:31: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3528:19: style: Variable 'curr_intv' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3712:47: style: Redundant condition: !(flags&1). 'flags&1 || (!(flags&1) && *s!=',')' is equivalent to 'flags&1 || *s!=','' [redundantCondition] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3935:41: style:inconclusive: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:1180:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. Rhtslib/src/htslib-1.18/hts.c:3935:41: note: Function 'hts_parse_reg64' argument 1 names different: declaration 'str' definition 's'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:3955:39: style:inconclusive: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:1190:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. Rhtslib/src/htslib-1.18/hts.c:3955:39: note: Function 'hts_parse_reg' argument 1 names different: declaration 'str' definition 's'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4054:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4088:53: style: Condition 'iter->end>beg' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/hts.c:4086:41: note: Assuming that condition 'beg>=iter->end' is not redundant Rhtslib/src/htslib-1.18/hts.c:4088:53: note: Condition 'iter->end>beg' is always true 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4105:20: style: Variable 'found_reg' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4194:32: style: Variable 'next_range' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4200:36: style: Local variable 'r' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/hts.c:4100:60: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:4200:36: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4225:32: style: Condition 'iter->in_off' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/hts.c:4192:25: note: Assuming that condition 'iter->i>=iter->n_off' is not redundant Rhtslib/src/htslib-1.18/hts.c:4225:32: note: Condition 'iter->in_off' is always true 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4255:40: style: Local variable 'r' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/hts.c:4100:60: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:4255:40: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4271:33: style: Local variable 'tid' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/hts.c:4103:14: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:4271:33: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4272:37: style: Local variable 'end' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/hts.c:4104:20: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:4272:37: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4348:50: error: Uninitialized variables: &key.reg, &key.intervals, &key.count, &key.min_beg, &key.max_end [uninitvar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4451:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4524:11: style: Variable 'csi_ext' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4525:11: style: Variable 'bai_ext' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4526:11: style: Variable 'tbi_ext' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4527:11: style: Variable 'crai_ext' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4528:11: style: Variable 'fai_ext' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4685:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4771:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4807:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4868:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:4944:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:527:30: style:inconclusive: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:544:37: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. Rhtslib/src/htslib-1.18/hts.c:527:30: note: Function 'hts_detect_format' argument 1 names different: declaration 'fp' definition 'hfile'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:532:31: style:inconclusive: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/hts.h:561:38: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. Rhtslib/src/htslib-1.18/hts.c:532:31: note: Function 'hts_detect_format2' argument 1 names different: declaration 'fp' definition 'hfile'. 2.19.0 Rhtslib/src/htslib-1.18/hts.c:603:15: style: Local variable 's' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/hts.c:535:19: note: Shadowed declaration Rhtslib/src/htslib-1.18/hts.c:603:15: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/hts.c:86:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_VERSION_TEXT [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/hts.c:932:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/htsfile.c:124:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/htsfile.c:163:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/htsfile.c:265:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/htsfile.c:52:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/htsfile.c:80:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/htslib/khash.h:401:24: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/test/sam.c:1134:5: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/sam.c:1134:5: note: Calling function 'kh_put_keep', 2nd argument 'strdup("chr3")' value is 0 Rhtslib/src/htslib-1.18/test/sam.c:48:1: note: Calling function '__ac_X31_hash_string', 1st argument 'key' value is 0 Rhtslib/src/htslib-1.18/htslib/khash.h:401:24: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/htslib/sam.h:1622:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/htslib/sam.h:1693:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] head Rhtslib/src/htslib-1.18/htslib/sam.h:259:25: error: syntax error [syntaxError] 2.19.0 Rhtslib/src/htslib-1.18/htslib/sam.h:966:50: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:111:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:112:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:205:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:216:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:41:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:42:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:43:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:48:27: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:58:51: style: Condition 'qual[z]>=13' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/realn.c:56:53: note: Assuming that condition 'qual[z]>=13' is not redundant Rhtslib/src/htslib-1.18/realn.c:58:51: note: Condition 'qual[z]>=13' is always true 2.19.0 Rhtslib/src/htslib-1.18/realn.c:73:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:77:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/realn.c:94:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1054:32: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1077:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:112:33: style:inconclusive: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:385:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. Rhtslib/src/htslib-1.18/sam.c:112:33: note: Function 'sam_hdr_destroy' argument 1 names different: declaration 'h' definition 'bh'. 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1179:14: style: Variable 'hb' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1189:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1387:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1562:17: style: Variable 's' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1587:11: style: Variable 'fd' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:1857:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2025:19: style: Variable 'tab' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2055:25: style: Local variable 'absent' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/sam.c:2020:20: note: Shadowed declaration Rhtslib/src/htslib-1.18/sam.c:2055:25: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2151:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2182:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2211:15: style: Variable 'text' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2285:32: style: Variable 'end' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2295:18: style: Variable 'tmp' can be declared as const array [constVariable] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2317:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2368:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:253:17: style: Condition 'bufsizel_text' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/sam.c:252:13: note: bufsize is assigned 'h->l_text+1' here. Rhtslib/src/htslib-1.18/sam.c:253:17: note: Condition 'bufsizel_text' is always false 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2540:43: style: Parameter 'tag_whitelist' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2544:23: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2645:19: style: Local variable 'end' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/sam.c:2539:48: note: Shadowed declaration Rhtslib/src/htslib-1.18/sam.c:2645:19: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2726:22: style: Variable 'q' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2760:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2777:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:2827:43: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/sam.c:2727:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/sam.c:2827:43: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3120:21: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3140:21: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3145:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EIO [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3242:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3316:34: 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] Rhtslib/src/htslib-1.18/sam.c:3452:42: note: You might need to cast the function pointer here Rhtslib/src/htslib-1.18/sam.c:3316:34: note: Parameter 'arg' can be declared as pointer to const 2.19.0 Rhtslib/src/htslib-1.18/sam.c:335:11: style: Variable 'text' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3397:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3405:19: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3406:19: style: Variable 'cp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3421:33: warning: Invalid test for overflow 'l->alloc>=l->alloc-line_frag'; signed integer overflow is undefined behavior. Some mainstream compilers removes handling of overflows when optimising the code and change the code to 'line_frag>=0'. [invalidTestForOverflow] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3508:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3659:14: style: Variable 'fp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3672:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:384:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3853:15: style: Variable 'bc' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3895:18: error: Dereferencing 's' after it is deallocated / released [deallocuse] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:3901:11: style: Variable 'name' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4031:57: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4036:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4071:17: style: Local variable 'ret' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/sam.c:4057:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/sam.c:4071:17: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4073:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4172:26: style: Variable 'x' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4183:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4203:14: style: Variable 's' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4203:18: style: Variable 'end' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4218:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4234:18: style: Local variable 's' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/sam.c:4203:14: note: Shadowed declaration Rhtslib/src/htslib-1.18/sam.c:4234:18: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/sam.c:425:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4275:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4300:15: warning: Either the condition 'x' is redundant or there is possible null pointer dereference: x. [nullPointerRedundantCheck] Rhtslib/src/htslib-1.18/sam.c:4304:9: note: Assuming that condition 'x' is not redundant Rhtslib/src/htslib-1.18/sam.c:4300:15: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4300:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4531:22: style: Variable 'x' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4553:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4624:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4667:14: style: Variable 'end' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4668:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4677:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4692:22: style: Variable 'e' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4704:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4711:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4721:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4738:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4740:39: style: Variable 'e' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4790:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4859:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4887:62: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4894:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4952:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4978:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4987:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:4994:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5004:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5014:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5056:11: style: Variable 'opts' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5114:50: style: Condition 'strncmp(format,"fa",format_len)==0' is always false [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5255:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5256:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5361:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:537:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5420:25: style: Local variable 'j' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/sam.c:5360:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/sam.c:5420:25: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5509:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:5508:29: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:5508:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:5509:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5510:18: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:5508:29: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:5508:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:5510:18: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5510:40: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:5508:29: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:5508:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:5510:40: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5510:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:5508:29: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:5508:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:5510:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5511:21: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:5508:29: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:5508:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:5511:21: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5511:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:5508:29: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:5508:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:5511:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5512:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:5508:29: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:5508:12: note: Assignment 'iter=(struct bam_plp_sbam_plp_t)calloc(1,sizeof(struct bam_plp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:5512:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5650:14: style: Variable 'a_seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5650:40: style: Variable 'b_seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5654:29: style: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value. [duplicateExpression] Rhtslib/src/htslib-1.18/sam.c:5652:31: note: 'iref' is assigned value 'b->core.pos' here. Rhtslib/src/htslib-1.18/sam.c:5654:29: note: Same expression on both sides of '-' because 'iref' and 'b->core.pos' represent the same value. 2.19.0 Rhtslib/src/htslib-1.18/sam.c:57:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:5833:39: style: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/sam.c:5833:39: note: Calling function 'resolve_cigar2' returns 1 Rhtslib/src/htslib-1.18/sam.c:5833:39: note: Condition 'resolve_cigar2(iter->plp+n_plp,iter->pos,&p->s)' is always true 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6011:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6011:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6012:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6012:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6013:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6013:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6014:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6014:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6015:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6015:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6016:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6016:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6017:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6017:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6018:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6018:5: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6020:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6020:9: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6021:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6021:24: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6021:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6021:9: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6022:24: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6022:24: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:6022:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iter [nullPointerOutOfMemory] Rhtslib/src/htslib-1.18/sam.c:6010:30: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/sam.c:6010:12: note: Assignment 'iter=(struct bam_mplp_sbam_mplp_t)calloc(1,sizeof(struct bam_mplp_s))', assigned value is 0 Rhtslib/src/htslib-1.18/sam.c:6022:9: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/sam.c:659:14: style: Variable 'CG' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:666:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:815:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam.c:909:27: style:inconclusive: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/sam.h:1115:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. Rhtslib/src/htslib-1.18/sam.c:909:27: note: Function 'bam_set_qname' argument 1 names different: declaration 'b' definition 'rec'. 2.19.0 Rhtslib/src/htslib-1.18/sam.c:916:17: style: Condition 'new_len<1' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/sam.c:915:36: note: Assignment 'new_len=strlen(qname)+1', assigned value is greater than 0 Rhtslib/src/htslib-1.18/sam.c:916:17: note: Condition 'new_len<1' is always false 2.19.0 Rhtslib/src/htslib-1.18/sam_internal.h:56:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/sam_internal.h:71:41: style: Parameter 'nib' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/sam_mods.c:205:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam_mods.c:247:14: style: Variable 'mi' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam_mods.c:263:14: style: Variable 'ml_end' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam_mods.c:273:18: style: Variable 'implicit' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/sam_mods.c:293:29: style: Variable 'me' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam_mods.c:477:15: style: Variable 'MMptr' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/sam_mods.c:635:44: style: Parameter 'state' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:110:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:199:52: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:375:81: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:382:15: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:413:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:496:11: style: Variable 'reheader' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:534:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:59:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:656:11: style: Variable 'suffix' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/tabix.c:71:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/fieldarith.c:37:14: style: Variable 'aux' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/fieldarith.c:42:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup.c:135:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup.c:180:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup.c:216:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup.c:81:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:100:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:101:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:138:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:149:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:150:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:155:13: style: Local variable 'n' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/test/pileup_mod.c:139:47: note: Shadowed declaration Rhtslib/src/htslib-1.18/test/pileup_mod.c:155:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:159:16: style: Variable 'n' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:49:32: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:60:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:61:18: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/pileup_mod.c:89:37: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:101:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1046:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1048:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1050:70: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1052:73: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1059:71: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1062:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1065:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1090:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1148:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1193:64: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1196:81: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1201:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1209:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1217:62: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1242:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1251:38: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1260:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1478:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1501:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1510:37: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources] Rhtslib/src/htslib-1.18/test/sam.c:1505:16: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/sam.c:1505:16: note: Assignment 'fin=fopen(filename,"rb")', assigned value is 0 Rhtslib/src/htslib-1.18/test/sam.c:1510:37: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1513:21: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources] Rhtslib/src/htslib-1.18/test/sam.c:1508:17: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/sam.c:1508:17: note: Assignment 'fout=fopen(tmpfilename,"wb")', assigned value is 0 Rhtslib/src/htslib-1.18/test/sam.c:1513:21: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1516:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources] Rhtslib/src/htslib-1.18/test/sam.c:1508:17: note: Assuming allocation function fails Rhtslib/src/htslib-1.18/test/sam.c:1508:17: note: Assignment 'fout=fopen(tmpfilename,"wb")', assigned value is 0 Rhtslib/src/htslib-1.18/test/sam.c:1516:12: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1584:24: style: The comparison 'no_compression != 0' is always false. [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1585:14: style: The comparison 'gzip != 1' is always false. [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1586:14: style: The comparison 'bgzf != 2' is always false. [knownConditionTrueFalse] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1703:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1925:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:1961:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2006:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2035:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2057:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2074:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2094:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2123:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2163:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2168:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2230:11: style: Variable 'cig' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:2235:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:318:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:443:15: style: The if condition is the same as the previous if condition [duplicateCondition] Rhtslib/src/htslib-1.18/test/sam.c:442:15: note: First condition Rhtslib/src/htslib-1.18/test/sam.c:443:15: note: Second condition 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:444:15: style: The if condition is the same as the previous if condition [duplicateCondition] Rhtslib/src/htslib-1.18/test/sam.c:443:15: note: First condition Rhtslib/src/htslib-1.18/test/sam.c:444:15: note: Second condition 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:445:15: style: The if condition is the same as the previous if condition [duplicateCondition] Rhtslib/src/htslib-1.18/test/sam.c:444:15: note: First condition Rhtslib/src/htslib-1.18/test/sam.c:445:15: note: Second condition 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:48:1: error: Uninitialized variable: val [legacyUninitvar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:498:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:64:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:763:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:766:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:770:49: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:773:55: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:781:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:784:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:787:52: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:851:9: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:901:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:956:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:960:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:964:63: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:967:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:970:69: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:980:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:983:61: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:992:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:996:27: warning: Either the condition '!text' is redundant or there is possible null pointer dereference: text. [nullPointerRedundantCheck] Rhtslib/src/htslib-1.18/test/sam.c:990:9: note: Assuming that condition '!text' is not redundant Rhtslib/src/htslib-1.18/test/sam.c:996:27: note: Null pointer dereference 2.19.0 Rhtslib/src/htslib-1.18/test/sam.c:99:39: style: Parameter 'aln' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test-bcf_set_variant_type.c:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test-parse-reg.c:172:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test-parse-reg.c:51:24: style: Parameter 'reg_exp' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test-parse-reg.c:63:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test-parse-reg.c:72:20: style: Parameter 'fn' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test-parse-reg.c:98:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_index.c:39:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_index.c:49:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_mod.c:120:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_mod.c:173:14: style: Variable 'all_mods' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test_realn.c:39:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_realn.c:45:11: style: Variable 'in_name' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test_realn.c:46:11: style: Variable 'out_name' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test_realn.c:47:11: style: Variable 'ref_name' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test_realn.c:49:10: style: Variable 'modew' can be declared as const array [constVariable] 2.19.0 Rhtslib/src/htslib-1.18/test/test_realn.c:60:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_view.c:199:29: style: Variable 'r' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/test/test_view.c:211:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_view.c:285:11: style: Variable 'out_fn' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/test/test_view.c:305:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/test/test_view.c:72:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:169:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:185:23: style: Variable 'lim' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:202:40: style: Parameter 'token' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:228:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:238:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:327:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:455:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/textutils.c:456:21: style: Variable 'bufend' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1121:38: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1128:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1178:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1226:31: style:inconclusive: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:596:35: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. Rhtslib/src/htslib-1.18/vcf.c:1226:31: note: Function 'bcf_hdr_append' argument 1 names different: declaration 'h' definition 'hdr'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1236:32: style:inconclusive: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:620:36: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. Rhtslib/src/htslib-1.18/vcf.c:1236:32: note: Function 'bcf_hdr_remove' argument 1 names different: declaration 'h' definition 'hdr'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1301:31: style:inconclusive: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:599:35: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. Rhtslib/src/htslib-1.18/vcf.c:1301:31: note: Function 'bcf_hdr_printf' argument 1 names different: declaration 'h' definition 'hdr'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1301:48: style:inconclusive: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:599:50: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. Rhtslib/src/htslib-1.18/vcf.c:1301:48: note: Function 'bcf_hdr_printf' argument 2 names different: declaration 'format' definition 'fmt'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1333:17: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1350:14: style: Variable 'hrec' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1428:34: style:inconclusive: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:340:38: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. Rhtslib/src/htslib-1.18/vcf.c:1428:34: note: Function 'bcf_hdr_read' argument 1 names different: declaration 'fp' definition 'hfp'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1467:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1482:28: style:inconclusive: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:376:32: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. Rhtslib/src/htslib-1.18/vcf.c:1482:28: note: Function 'bcf_hdr_write' argument 1 names different: declaration 'fp' definition 'hfp'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1485:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:158:35: style:inconclusive: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:571:39: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. Rhtslib/src/htslib-1.18/vcf.c:158:35: note: Function 'bcf_hdr_add_sample' argument 1 names different: declaration 'hdr' definition 'h'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:158:50: style:inconclusive: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:571:56: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. Rhtslib/src/htslib-1.18/vcf.c:158:50: note: Function 'bcf_hdr_add_sample' argument 2 names different: declaration 'sample' definition 's'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1621:57: style: Parameter 'end' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1677:64: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1709:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1774:19: style: Variable 'id_tmp' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1859:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1897:45: style:inconclusive: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:506:49: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. Rhtslib/src/htslib-1.18/vcf.c:1897:45: note: Function 'bcf_readrec' argument 3 names different: declaration 'v' definition 'vv'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1907:40: style: Parameter 'line' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1921:78: style: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false [knownConditionTrueFalse] Rhtslib/src/htslib-1.18/vcf.c:1921:26: note: Calling function 'bcf_enc_vchar' returns 0 Rhtslib/src/htslib-1.18/vcf.c:1921:78: note: Condition 'bcf_enc_vchar(str,strlen(line->d.allele[i]),line->d.allele[i])<0' is always false 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1943:21: style: Variable 'info' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:1963:11: style: Variable 'shared_ori' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2065:24: style: Variable 'fmt' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2139:24: style:inconclusive: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:452:28: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. Rhtslib/src/htslib-1.18/vcf.c:2139:24: note: Function 'bcf_write' argument 1 names different: declaration 'fp' definition 'hfp'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:217:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2215:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2250:23: style: Variable 'tab' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2286:25: style: Variable 'hrec' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2332:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2395:56: style:inconclusive: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:645:60: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. Rhtslib/src/htslib-1.18/vcf.c:2395:56: note: Function 'bcf_hdr_seqnames' argument 2 names different: declaration 'nseqs' definition 'n'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2415:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:242:38: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2462:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2550:48: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2638:40: style: Parameter 's' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2638:80: style: Parameter 'p' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2652:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2687:17: style: Local variable 'l' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/vcf.c:2644:12: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcf.c:2687:17: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2706:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable info [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:280:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2899:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2958:28: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:296:34: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:2982:43: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3024:22: style: Variable 'res' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:303:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3048:19: style: Variable 'max_n_flt' is assigned a value that is never used. [unreadVariable] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:318:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3229:32: portability: Casting between signed int * and float * which have an incompatible binary data representation. [invalidPointerCast] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3257:23: style: Variable 't' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3432:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:344:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3489:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3568:13: style: Local variable 'i' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/vcf.c:3483:9: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcf.c:3568:13: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3623:56: style: Parameter 'v' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3655:37: style:inconclusive: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:1202:41: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. Rhtslib/src/htslib-1.18/vcf.c:3655:37: note: Function 'bcf_hdr_id2int' argument 1 names different: declaration 'hdr' definition 'h'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3655:44: style:inconclusive: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:1202:50: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. Rhtslib/src/htslib-1.18/vcf.c:3655:44: note: Function 'bcf_hdr_id2int' argument 2 names different: declaration 'type' definition 'which'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3678:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3791:49: style: Parameter 'h' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3818:35: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3889:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3902:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3911:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3912:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:393:35: style: Parameter 'hrec' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3982:29: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:3995:25: style: Variable 'rec' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4004:26: style: Variable 'd_src' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4005:26: style: Variable 'd_dst' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4027:73: style:inconclusive: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. [funcArgNamesDifferent] Rhtslib/src/htslib-1.18/htslib/vcf.h:790:77: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. Rhtslib/src/htslib-1.18/vcf.c:4027:73: note: Function 'bcf_translate' argument 3 names different: declaration 'src_line' definition 'line'. 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4045:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4207:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4286:16: style: Local variable 'samples' shadows outer argument [shadowArgument] Rhtslib/src/htslib-1.18/vcf.c:4227:53: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcf.c:4286:16: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4315:17: style: Local variable 'k' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/vcf.c:4288:13: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcf.c:4315:17: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4335:59: style: Parameter 'imap' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4346:24: style: Variable 'f' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4484:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4495:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4558:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4717:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:479:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4824:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4845:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4863:62: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4867:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:4883:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:489:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:500:15: style: Variable 'val' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:5039:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:5046:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:5076:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:5160:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:5187:18: style: Variable 'src' can be declared as pointer to const [constVariablePointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:5199:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:568:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:577:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:583:20: style: Redundant condition: The condition '*q' is redundant since '*q == ' '' is sufficient. [redundantCondition] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:677:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:729:17: style: Local variable 'k' shadows outer variable [shadowVariable] Rhtslib/src/htslib-1.18/vcf.c:704:13: note: Shadowed declaration Rhtslib/src/htslib-1.18/vcf.c:729:17: note: Shadow variable 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:907:50: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:948:36: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer] 2.19.0 Rhtslib/src/htslib-1.18/vcf.c:970:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable] DONE