2025-09-15 11:58
ftp://ftp.de.debian.org/debian/pool/main/p/python-pysam/python-pysam_0.23.0+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1
platform: Linux-6.8.0-79-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.69
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0
cppcheck: head 2.18.0
head-info: 3e169d6 (2025-09-15 13:38:15 +0200)
count: 2499 2499
elapsed-time: 300.3 308.2
head-timing-info:

old-timing-info:

head results:
pysam-0.23.0/bcftools/HMM.c:95:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:95:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:95:29: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:95:29: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:97:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:97:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:99:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:99:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:101:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:101:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:104:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:104:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:131:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:131:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:132:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:132:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:133:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:133:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:156:9: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:154:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:154:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:155:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c:156:9: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:157:9: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:154:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:154:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:155:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c:157:9: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:158:9: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:154:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:154:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:155:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c:158:9: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:158:30: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:154:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:154:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:155:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c:158:30: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:160:5: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:154:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:154:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:155:20: note: Assignment 'snapshot=(struct snapshot_t*)mem', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:160:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:191:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:191:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:194:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:194:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:197:12: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:197:12: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:197:48: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:197:48: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:197:61: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:197:61: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:25: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:25: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:39: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:39: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:55: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:55: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:76: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:76: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:89: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:89: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:103: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:103: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:120: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:120: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:133: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:133: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:201:147: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c:201:147: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c:157:45: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:154:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:154:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:157:45: note: Null pointer addition
pysam-0.23.0/bcftools/HMM.c:157:30: portability: Casting between unsigned char * and double * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/HMM.c:139:38: style:inconclusive: Function 'hmm_snapshot' argument 2 names different: declaration 'snapshot' definition '_snapshot'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:66:38: note: Function 'hmm_snapshot' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c:139:38: note: Function 'hmm_snapshot' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c:164:36: style:inconclusive: Function 'hmm_restore' argument 2 names different: declaration 'snapshot' definition '_snapshot'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:75:36: note: Function 'hmm_restore' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c:164:36: note: Function 'hmm_restore' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c:180:34: style:inconclusive: Function 'hmm_reset' argument 2 names different: declaration 'snapshot' definition '_snapshot'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:76:34: note: Function 'hmm_reset' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c:180:34: note: Function 'hmm_reset' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c:227:38: style:inconclusive: Function 'hmm_run_viterbi' argument 2 names different: declaration 'nsites' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:101:38: note: Function 'hmm_run_viterbi' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c:227:38: note: Function 'hmm_run_viterbi' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c:227:49: style:inconclusive: Function 'hmm_run_viterbi' argument 3 names different: declaration 'eprob' definition 'eprobs'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:101:54: note: Function 'hmm_run_viterbi' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c:227:49: note: Function 'hmm_run_viterbi' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c:292:38: style:inconclusive: Function 'hmm_run_fwd_bwd' argument 2 names different: declaration 'nsites' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:115:38: note: Function 'hmm_run_fwd_bwd' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c:292:38: note: Function 'hmm_run_fwd_bwd' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c:292:49: style:inconclusive: Function 'hmm_run_fwd_bwd' argument 3 names different: declaration 'eprob' definition 'eprobs'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:115:54: note: Function 'hmm_run_fwd_bwd' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c:292:49: note: Function 'hmm_run_fwd_bwd' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c:375:44: style:inconclusive: Function 'hmm_run_baum_welch' argument 2 names different: declaration 'nsites' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:133:44: note: Function 'hmm_run_baum_welch' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c:375:44: note: Function 'hmm_run_baum_welch' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c:375:55: style:inconclusive: Function 'hmm_run_baum_welch' argument 3 names different: declaration 'eprob' definition 'eprobs'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:133:60: note: Function 'hmm_run_baum_welch' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c:375:55: note: Function 'hmm_run_baum_welch' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c:68:38: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:69:30: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:70:28: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:71:37: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:73:51: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:73:62: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:93:42: style: Parameter 'probs' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:166:17: style: Variable 'snapshot' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c:189:40: style: Parameter 'tprob' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:250:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c:315:17: style: Variable 'fwd_prev' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c:317:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c:346:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c:403:17: style: Variable 'fwd_prev' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c:405:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c:431:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:97:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:137:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:97:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:97:29: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:137:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:97:29: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:99:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:137:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:99:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:101:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:137:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:101:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:103:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:137:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:103:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:106:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:137:21: note: Calling function 'hmm_init_states', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:106:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:133:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:133:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:134:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:134:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:135:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:135:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:158:9: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:157:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c.pysam.c:158:9: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:159:9: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:157:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c.pysam.c:159:9: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:160:9: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:157:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c.pysam.c:160:9: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:160:30: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:157:18: note: snapshot is assigned '(struct snapshot_t*)mem' here.
pysam-0.23.0/bcftools/HMM.c.pysam.c:160:30: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:162:5: warning: If memory allocation fails, then there is a possible null pointer dereference: snapshot [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:157:20: note: Assignment 'snapshot=(struct snapshot_t*)mem', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:162:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:193:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:193:5: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:196:11: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:196:11: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:199:12: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:199:12: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:199:48: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:199:48: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:199:61: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:199:61: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:25: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:25: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:39: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:39: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:55: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:55: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:76: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:76: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:89: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:89: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:103: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:103: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:120: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:120: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:133: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:133: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:147: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:132:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:136:19: note: Calling function 'hmm_set_tprob', 1st argument 'hmm' value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:203:147: note: Null pointer dereference
pysam-0.23.0/bcftools/HMM.c.pysam.c:159:45: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c.pysam.c:156:24: note: Assignment 'mem=(uint8_t*)malloc(str_size+pad_size+dbl_size*2*hmm->nstates)', assigned value is 0
pysam-0.23.0/bcftools/HMM.c.pysam.c:159:45: note: Null pointer addition
pysam-0.23.0/bcftools/HMM.c.pysam.c:159:30: portability: Casting between unsigned char * and double * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/HMM.c.pysam.c:141:38: style:inconclusive: Function 'hmm_snapshot' argument 2 names different: declaration 'snapshot' definition '_snapshot'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:66:38: note: Function 'hmm_snapshot' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:141:38: note: Function 'hmm_snapshot' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:166:36: style:inconclusive: Function 'hmm_restore' argument 2 names different: declaration 'snapshot' definition '_snapshot'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:75:36: note: Function 'hmm_restore' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:166:36: note: Function 'hmm_restore' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:182:34: style:inconclusive: Function 'hmm_reset' argument 2 names different: declaration 'snapshot' definition '_snapshot'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:76:34: note: Function 'hmm_reset' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:182:34: note: Function 'hmm_reset' argument 2 names different: declaration 'snapshot' definition '_snapshot'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:229:38: style:inconclusive: Function 'hmm_run_viterbi' argument 2 names different: declaration 'nsites' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:101:38: note: Function 'hmm_run_viterbi' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:229:38: note: Function 'hmm_run_viterbi' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:229:49: style:inconclusive: Function 'hmm_run_viterbi' argument 3 names different: declaration 'eprob' definition 'eprobs'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:101:54: note: Function 'hmm_run_viterbi' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:229:49: note: Function 'hmm_run_viterbi' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:294:38: style:inconclusive: Function 'hmm_run_fwd_bwd' argument 2 names different: declaration 'nsites' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:115:38: note: Function 'hmm_run_fwd_bwd' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:294:38: note: Function 'hmm_run_fwd_bwd' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:294:49: style:inconclusive: Function 'hmm_run_fwd_bwd' argument 3 names different: declaration 'eprob' definition 'eprobs'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:115:54: note: Function 'hmm_run_fwd_bwd' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:294:49: note: Function 'hmm_run_fwd_bwd' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:377:44: style:inconclusive: Function 'hmm_run_baum_welch' argument 2 names different: declaration 'nsites' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:133:44: note: Function 'hmm_run_baum_welch' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:377:44: note: Function 'hmm_run_baum_welch' argument 2 names different: declaration 'nsites' definition 'n'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:377:55: style:inconclusive: Function 'hmm_run_baum_welch' argument 3 names different: declaration 'eprob' definition 'eprobs'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/HMM.h:133:60: note: Function 'hmm_run_baum_welch' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:377:55: note: Function 'hmm_run_baum_welch' argument 3 names different: declaration 'eprob' definition 'eprobs'.
pysam-0.23.0/bcftools/HMM.c.pysam.c:70:38: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:71:30: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:72:28: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:73:37: style: Parameter 'hmm' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:75:51: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:75:62: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:95:42: style: Parameter 'probs' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:168:17: style: Variable 'snapshot' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:191:40: style: Parameter 'tprob' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:252:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:317:17: style: Variable 'fwd_prev' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:319:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:348:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:405:17: style: Variable 'fwd_prev' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:407:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/HMM.c.pysam.c:433:17: style: Variable 'eprob' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c:97:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c:350:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c:468:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c:516:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c:544:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c:815:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c:846:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c:363:27: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/abuf.c:359:27: note: First condition
pysam-0.23.0/bcftools/abuf.c:363:27: note: Second condition
pysam-0.23.0/bcftools/abuf.c:570:27: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/abuf.c:568:27: note: First condition
pysam-0.23.0/bcftools/abuf.c:570:27: note: Second condition
pysam-0.23.0/bcftools/abuf.c:84:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c:83:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c:83:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c:84:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c:85:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c:83:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c:83:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c:85:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c:86:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c:83:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c:83:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c:86:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c:87:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c:83:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c:83:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c:87:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c:472:9: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
pysam-0.23.0/bcftools/abuf.c:473:9: note: Found duplicate branches for 'if' and 'else'.
pysam-0.23.0/bcftools/abuf.c:472:9: note: Found duplicate branches for 'if' and 'else'.
pysam-0.23.0/bcftools/abuf.c:765:13: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/abuf.c:761:11: note: Shadowed declaration
pysam-0.23.0/bcftools/abuf.c:765:13: note: Shadow variable
pysam-0.23.0/bcftools/abuf.c:774:13: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/abuf.c:761:11: note: Shadowed declaration
pysam-0.23.0/bcftools/abuf.c:774:13: note: Shadow variable
pysam-0.23.0/bcftools/bcftools.h:119:40: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/abuf.c:269:65: style: Parameter 'atom' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/abuf.c:428:26: style: Variable 'tbl' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c:482:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c:614:23: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c:659:30: style: Variable 'tbl' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c:710:35: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c:720:35: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/abuf.c:795:21: style: Variable 'out' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/bcftools.h:172:45: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/rbuf.h:51:36: style: Parameter 'rbuf' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/rbuf.h:76:39: style: Parameter 'rbuf' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/rbuf.h:100:37: style: Parameter 'rbuf' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/abuf.c:396:49: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:399:42: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:401:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:422:49: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:423:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:425:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:425:51: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:435:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:614:39: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:615:39: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:616:48: portability: 'src' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:619:35: portability: 'src' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:621:31: portability: 'dst' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:640:47: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:642:43: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:653:39: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:654:39: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:656:27: portability: 'dst' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:656:40: portability: 'src' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c:664:31: portability: 'dst' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:99:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c.pysam.c:352:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c.pysam.c:470:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c.pysam.c:518:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c.pysam.c:546:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c.pysam.c:817:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c.pysam.c:848:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/abuf.c.pysam.c:365:27: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/abuf.c.pysam.c:361:27: note: First condition
pysam-0.23.0/bcftools/abuf.c.pysam.c:365:27: note: Second condition
pysam-0.23.0/bcftools/abuf.c.pysam.c:572:27: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/abuf.c.pysam.c:570:27: note: First condition
pysam-0.23.0/bcftools/abuf.c.pysam.c:572:27: note: Second condition
pysam-0.23.0/bcftools/abuf.c.pysam.c:86:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c.pysam.c:86:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c.pysam.c:87:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c.pysam.c:87:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c.pysam.c:88:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c.pysam.c:88:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c.pysam.c:89:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/abuf.c.pysam.c:85:19: note: Assignment 'buf=(struct abuf_t*)calloc(1,sizeof(struct abuf_t))', assigned value is 0
pysam-0.23.0/bcftools/abuf.c.pysam.c:89:5: note: Null pointer dereference
pysam-0.23.0/bcftools/abuf.c.pysam.c:474:9: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
pysam-0.23.0/bcftools/abuf.c.pysam.c:475:9: note: Found duplicate branches for 'if' and 'else'.
pysam-0.23.0/bcftools/abuf.c.pysam.c:474:9: note: Found duplicate branches for 'if' and 'else'.
pysam-0.23.0/bcftools/abuf.c.pysam.c:767:13: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/abuf.c.pysam.c:763:11: note: Shadowed declaration
pysam-0.23.0/bcftools/abuf.c.pysam.c:767:13: note: Shadow variable
pysam-0.23.0/bcftools/abuf.c.pysam.c:776:13: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/abuf.c.pysam.c:763:11: note: Shadowed declaration
pysam-0.23.0/bcftools/abuf.c.pysam.c:776:13: note: Shadow variable
pysam-0.23.0/bcftools/abuf.c.pysam.c:271:65: style: Parameter 'atom' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:430:26: style: Variable 'tbl' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:484:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:616:23: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:661:30: style: Variable 'tbl' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:712:35: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:722:35: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:797:21: style: Variable 'out' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:398:49: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:401:42: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:403:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:424:49: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:425:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:427:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:427:51: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:437:33: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:616:39: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:617:39: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:618:48: portability: 'src' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:621:35: portability: 'src' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:623:31: portability: 'dst' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:642:47: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:644:43: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:655:39: portability: 'buf->tmp' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:656:39: portability: 'buf->tmp2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:658:27: portability: 'dst' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:658:40: portability: 'src' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/abuf.c.pysam.c:666:31: portability: 'dst' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
pysam-0.23.0/bcftools/bam2bcf.c:99:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nm [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:152:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:264:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:617:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:664:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:727:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:777:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:848:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:893:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:960:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:1180:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable two [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c:886:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/bam2bcf.c:888:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/bam2bcf.c:476:23: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c:480:32: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c:482:32: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c:484:32: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c:49:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:49:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:50:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:50:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:50:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:50:22: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:50:38: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:50:38: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:51:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:51:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:52:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:52:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:53:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:53:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:54:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:54:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:55:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:55:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:56:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:56:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:57:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:57:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:58:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:58:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:59:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:59:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:59:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:59:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:60:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:60:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:60:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:60:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:61:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:61:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:61:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:61:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:62:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:62:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:62:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:62:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:63:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:63:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:64:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:64:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:64:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:64:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:65:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:65:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:65:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:65:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:66:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:66:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:66:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:66:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:67:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:67:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:67:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:67:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:68:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:68:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:68:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:68:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:69:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:69:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:69:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:69:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:70:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:70:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:70:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:70:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:71:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:71:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:71:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c:48:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c:48:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c:71:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c:1178:42: style:inconclusive: Function 'bcf_call2bcf' argument 2 names different: declaration 'b' definition 'rec'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bam2bcf.h:195:46: note: Function 'bcf_call2bcf' argument 2 names different: declaration 'b' definition 'rec'.
pysam-0.23.0/bcftools/bam2bcf.c:1178:42: note: Function 'bcf_call2bcf' argument 2 names different: declaration 'b' definition 'rec'.
pysam-0.23.0/bcftools/bam2bcf.c:1071:21: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/bam2bcf.c:975:21: note: Shadowed declaration
pysam-0.23.0/bcftools/bam2bcf.c:1071:21: note: Shadow variable
pysam-0.23.0/bcftools/bam2bcf.c:1101:21: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/bam2bcf.c:975:21: note: Shadowed declaration
pysam-0.23.0/bcftools/bam2bcf.c:1101:21: note: Shadow variable
pysam-0.23.0/bcftools/bam2bcf.c:425:22: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/bam2bcf.c:596:22: style: Parameter 'pos' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:659:29: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:659:37: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:711:31: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:711:39: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:756:27: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:756:35: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:813:28: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c:813:36: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:101:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nm [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:154:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:266:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:619:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:666:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:729:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:779:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:850:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:895:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:962:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:1182:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable two [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:888:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:890:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:478:23: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:482:32: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:484:32: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:486:32: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:51:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:51:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:52:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:52:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:52:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:52:22: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:52:38: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:52:38: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:53:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:53:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:54:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:54:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:55:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:55:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:56:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:56:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:57:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:57:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:58:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:58:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:59:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:59:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:60:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:60:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:61:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:61:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:61:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:61:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:62:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:62:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:62:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:62:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:63:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:63:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:63:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:63:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:64:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:64:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:64:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:64:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:65:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:65:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:66:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:66:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:66:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:66:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:67:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:67:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:67:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:67:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:68:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:68:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:68:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:68:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:69:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:69:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:69:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:69:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:70:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:70:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:70:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:70:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:71:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:71:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:71:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:71:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:72:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:72:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:72:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:72:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:73:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:73:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:73:34: warning: If memory allocation fails, then there is a possible null pointer dereference: bca [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:50:11: note: Assignment 'bca=(struct bcf_callaux_t*)calloc(1,sizeof(struct bcf_callaux_t))', assigned value is 0
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:73:34: note: Null pointer dereference
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:1180:42: style:inconclusive: Function 'bcf_call2bcf' argument 2 names different: declaration 'b' definition 'rec'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bam2bcf.h:195:46: note: Function 'bcf_call2bcf' argument 2 names different: declaration 'b' definition 'rec'.
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:1180:42: note: Function 'bcf_call2bcf' argument 2 names different: declaration 'b' definition 'rec'.
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:1073:21: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:977:21: note: Shadowed declaration
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:1073:21: note: Shadow variable
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:1103:21: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:977:21: note: Shadowed declaration
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:1103:21: note: Shadow variable
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:427:22: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:598:22: style: Parameter 'pos' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:661:29: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:661:37: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:713:31: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:713:39: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:758:27: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:758:35: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:815:28: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf.c.pysam.c:815:36: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bam2bcf_edlib.c:46:1: error: There is an unknown macro here somewhere. Configuration is required. If KSORT_INIT_STATIC_GENERIC is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/bam2bcf_edlib.c.pysam.c:48:1: error: There is an unknown macro here somewhere. Configuration is required. If KSORT_INIT_STATIC_GENERIC is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/bam2bcf_iaux.c:39:1: error: There is an unknown macro here somewhere. Configuration is required. If KSORT_INIT_STATIC_GENERIC is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/bam2bcf_iaux.c.pysam.c:41:1: error: There is an unknown macro here somewhere. Configuration is required. If KSORT_INIT_STATIC_GENERIC is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/bam2bcf_indel.c:37:1: error: There is an unknown macro here somewhere. Configuration is required. If KSORT_INIT_GENERIC is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/bam2bcf_indel.c.pysam.c:39:1: error: There is an unknown macro here somewhere. Configuration is required. If KSORT_INIT_GENERIC is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/bam_sample.c:62:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bsmpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam_sample.c:61:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam_sample.c:61:13: note: Assignment 'bsmpl=(struct bam_smpl_t*)calloc(1,sizeof(struct bam_smpl_t))', assigned value is 0
pysam-0.23.0/bcftools/bam_sample.c:62:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bam_sample.c.pysam.c:64:5: warning: If memory allocation fails, then there is a possible null pointer dereference: bsmpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/bam_sample.c.pysam.c:63:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/bam_sample.c.pysam.c:63:13: note: Assignment 'bsmpl=(struct bam_smpl_t*)calloc(1,sizeof(struct bam_smpl_t))', assigned value is 0
pysam-0.23.0/bcftools/bam_sample.c.pysam.c:64:5: note: Null pointer dereference
pysam-0.23.0/bcftools/bcftools.pysam.c:54:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bcftools.pysam.c:70:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/bin.c:38:29: style:inconclusive: Function 'bin_init' argument 1 names different: declaration 'list' definition 'list_def'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bin.h:45:29: note: Function 'bin_init' argument 1 names different: declaration 'list' definition 'list_def'.
pysam-0.23.0/bcftools/bin.c:38:29: note: Function 'bin_init' argument 1 names different: declaration 'list' definition 'list_def'.
pysam-0.23.0/bcftools/bin.c:88:37: style:inconclusive: Function 'bin_get_value' argument 2 names different: declaration 'ith' definition 'idx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bin.h:62:37: note: Function 'bin_get_value' argument 2 names different: declaration 'ith' definition 'idx'.
pysam-0.23.0/bcftools/bin.c:88:37: note: Function 'bin_get_value' argument 2 names different: declaration 'ith' definition 'idx'.
pysam-0.23.0/bcftools/bin.c:86:25: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bin.c:90:24: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bin.c.pysam.c:40:29: style:inconclusive: Function 'bin_init' argument 1 names different: declaration 'list' definition 'list_def'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bin.h:45:29: note: Function 'bin_init' argument 1 names different: declaration 'list' definition 'list_def'.
pysam-0.23.0/bcftools/bin.c.pysam.c:40:29: note: Function 'bin_init' argument 1 names different: declaration 'list' definition 'list_def'.
pysam-0.23.0/bcftools/bin.c.pysam.c:90:37: style:inconclusive: Function 'bin_get_value' argument 2 names different: declaration 'ith' definition 'idx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bin.h:62:37: note: Function 'bin_get_value' argument 2 names different: declaration 'ith' definition 'idx'.
pysam-0.23.0/bcftools/bin.c.pysam.c:90:37: note: Function 'bin_get_value' argument 2 names different: declaration 'ith' definition 'idx'.
pysam-0.23.0/bcftools/bin.c.pysam.c:88:25: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/bin.c.pysam.c:92:24: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ccall.c:105:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ccall.c:117:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable two [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ccall.c:260:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ccall.c:333:9: style: Redundant initialization for 'ret'. The initialized value is overwritten before it is read. [redundantInitialization]
pysam-0.23.0/bcftools/ccall.c:329:13: note: ret is initialized
pysam-0.23.0/bcftools/ccall.c:333:9: note: ret is overwritten
pysam-0.23.0/bcftools/ccall.c:90:30: style: Parameter 'pl2p' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ccall.c:103:43: style: Parameter 'a' can be declared as const array [constParameter]
pysam-0.23.0/bcftools/ccall.c:139:81: style: Parameter 'em' can be declared as const array [constParameter]
pysam-0.23.0/bcftools/ccall.c:178:18: style: Variable 'p1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/ccall.c.pysam.c:107:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ccall.c.pysam.c:119:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable two [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ccall.c.pysam.c:262:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ccall.c.pysam.c:335:9: style: Redundant initialization for 'ret'. The initialized value is overwritten before it is read. [redundantInitialization]
pysam-0.23.0/bcftools/ccall.c.pysam.c:331:13: note: ret is initialized
pysam-0.23.0/bcftools/ccall.c.pysam.c:335:9: note: ret is overwritten
pysam-0.23.0/bcftools/ccall.c.pysam.c:92:30: style: Parameter 'pl2p' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ccall.c.pysam.c:105:43: style: Parameter 'a' can be declared as const array [constParameter]
pysam-0.23.0/bcftools/ccall.c.pysam.c:141:81: style: Parameter 'em' can be declared as const array [constParameter]
pysam-0.23.0/bcftools/ccall.c.pysam.c:180:18: style: Variable 'p1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/cols.c:31:10: warning: If memory allocation fails, then there is a possible null pointer dereference: cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:30:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:30:25: note: Assignment 'cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:31:10: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:38:18: warning: If memory allocation fails, then there is a possible null pointer dereference: se [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:33:24: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:33:24: note: Assignment 'cols->rmme=strdup(line)', assigned value is 0
pysam-0.23.0/bcftools/cols.c:34:20: note: Assignment 'ss=cols->rmme', assigned value is 0
pysam-0.23.0/bcftools/cols.c:37:20: note: Assignment 'se=ss', assigned value is 0
pysam-0.23.0/bcftools/cols.c:38:18: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:63:9: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:62:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:62:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:63:9: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:64:9: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:62:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:62:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:64:9: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:66:21: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:62:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:62:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:66:21: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:72:13: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:62:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:62:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:72:13: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:76:9: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:62:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:62:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:76:9: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:80:22: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:62:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:62:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:80:22: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c:81:22: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c:62:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c:62:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c:81:22: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:33:10: warning: If memory allocation fails, then there is a possible null pointer dereference: cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:32:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:32:25: note: Assignment 'cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:33:10: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:40:18: warning: If memory allocation fails, then there is a possible null pointer dereference: se [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:35:24: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:35:24: note: Assignment 'cols->rmme=strdup(line)', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:36:20: note: Assignment 'ss=cols->rmme', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:39:20: note: Assignment 'se=ss', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:40:18: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:65:9: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:64:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:64:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:65:9: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:66:9: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:64:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:64:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:66:9: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:68:21: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:64:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:64:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:68:21: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:74:13: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:64:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:64:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:74:13: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:78:9: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:64:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:64:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:78:9: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:82:22: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:64:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:64:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:82:22: note: Null pointer dereference
pysam-0.23.0/bcftools/cols.c.pysam.c:83:22: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_cols [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/cols.c.pysam.c:64:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/cols.c.pysam.c:64:28: note: Assignment 'tmp_cols=(struct cols_t*)calloc(1,sizeof(struct cols_t))', assigned value is 0
pysam-0.23.0/bcftools/cols.c.pysam.c:83:22: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:229:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:363:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:412:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buffer [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:420:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:544:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:565:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_RESIZE_CLEAR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:608:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:1100:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:1172:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:1241:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c:521:19: style: Expression is always false because 'else if' condition matches previous condition at line 516. [multiCondition]
pysam-0.23.0/bcftools/consensus.c:350:29: style: Redundant condition: The condition '!*se' is redundant since '*se != '-'' is sufficient. [redundantCondition]
pysam-0.23.0/bcftools/consensus.c:240:19: style: Condition 'args->sample' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/consensus.c:140:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:139:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:139:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:140:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:141:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:139:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:139:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:141:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:142:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:139:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:139:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:142:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:143:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:139:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:139:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:143:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:144:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:139:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:139:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:144:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:145:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:139:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:139:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:145:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:146:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:139:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:139:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:146:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:493:25: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:481:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:481:23: note: Assignment 'out=malloc(rlen+1)', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:493:25: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:494:5: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:481:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:481:23: note: Assignment 'out=malloc(rlen+1)', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:494:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:1219:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:1218:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:1218:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:1219:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:1219:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:1218:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:1218:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:1219:26: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:1220:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c:1218:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c:1218:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c:1220:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c:185:11: style: Redundant initialization for 'n'. The initialized value is overwritten before it is read. [redundantInitialization]
pysam-0.23.0/bcftools/consensus.c:180:11: note: n is initialized
pysam-0.23.0/bcftools/consensus.c:185:11: note: n is overwritten
pysam-0.23.0/bcftools/consensus.c:735:13: style: Local variable 'ialt' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/consensus.c:605:9: note: Shadowed declaration
pysam-0.23.0/bcftools/consensus.c:735:13: note: Shadow variable
pysam-0.23.0/bcftools/consensus.c:304:47: style: Parameter 'with' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c:341:11: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/consensus.c:473:46: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c:479:29: style: Parameter 'ref' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c:479:50: style: Parameter 'alt' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c:497:28: style: Parameter 'ref' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c:507:28: style: Parameter 'ref' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c:595:15: style: Variable 'chr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/consensus.c:609:20: style: Variable 'fmt' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/consensus.c:1222:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/consensus.c:760:18: style: Variable 'ialt' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/consensus.c.pysam.c:231:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:388:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:414:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buffer [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:422:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:546:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:567:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_RESIZE_CLEAR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:610:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:1102:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:1243:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/consensus.c.pysam.c:523:19: style: Expression is always false because 'else if' condition matches previous condition at line 518. [multiCondition]
pysam-0.23.0/bcftools/consensus.c.pysam.c:352:29: style: Redundant condition: The condition '!*se' is redundant since '*se != '-'' is sufficient. [redundantCondition]
pysam-0.23.0/bcftools/consensus.c.pysam.c:242:19: style: Condition 'args->sample' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/consensus.c.pysam.c:142:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:142:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:143:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:143:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:144:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:144:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:145:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:145:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:146:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:146:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:147:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:147:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:148:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chain [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:141:13: note: Assignment 'chain=(struct chain_t*)calloc(1,sizeof(struct chain_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:148:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:495:25: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:483:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:483:23: note: Assignment 'out=malloc(rlen+1)', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:495:25: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:496:5: warning: If memory allocation fails, then there is a possible null pointer dereference: out [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:483:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:483:23: note: Assignment 'out=malloc(rlen+1)', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:496:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:1221:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:1220:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:1220:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:1221:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:1221:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:1220:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:1220:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:1221:26: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:1222:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/consensus.c.pysam.c:1220:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/consensus.c.pysam.c:1220:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/consensus.c.pysam.c:1222:5: note: Null pointer dereference
pysam-0.23.0/bcftools/consensus.c.pysam.c:187:11: style: Redundant initialization for 'n'. The initialized value is overwritten before it is read. [redundantInitialization]
pysam-0.23.0/bcftools/consensus.c.pysam.c:182:11: note: n is initialized
pysam-0.23.0/bcftools/consensus.c.pysam.c:187:11: note: n is overwritten
pysam-0.23.0/bcftools/consensus.c.pysam.c:737:13: style: Local variable 'ialt' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/consensus.c.pysam.c:607:9: note: Shadowed declaration
pysam-0.23.0/bcftools/consensus.c.pysam.c:737:13: note: Shadow variable
pysam-0.23.0/bcftools/consensus.c.pysam.c:306:47: style: Parameter 'with' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:343:11: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:475:46: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:481:29: style: Parameter 'ref' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:481:50: style: Parameter 'alt' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:499:28: style: Parameter 'ref' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:509:28: style: Parameter 'ref' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:597:15: style: Variable 'chr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:611:20: style: Variable 'fmt' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/consensus.c.pysam.c:1224:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/consensus.c.pysam.c:762:18: style: Variable 'ialt' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/hex.h:58:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIx64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/variantkey.h:179:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu8 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:126:130: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:175:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:182:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_INT8 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:228:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:315:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:341:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:390:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_FLOAT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:437:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_INT8 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:599:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_INT8 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:639:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_SNP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:647:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_REF [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:670:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:690:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:741:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:790:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:842:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:996:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:1123:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIx32 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:1136:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:1170:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:1272:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:1388:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:1511:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:1660:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c:201:16: style: Array index 'ibeg' is used before limits check. [arrayIndexThenCheck]
pysam-0.23.0/bcftools/convert.c:1509:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c:1508:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c:1508:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c:1509:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c:1510:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c:1508:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c:1508:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c:1510:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c:1511:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c:1508:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c:1508:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c:1511:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c:1512:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c:1508:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c:1508:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c:1512:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c:1515:15: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c:1508:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c:1508:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c:1515:15: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c:1506:81: style:inconclusive: Function 'convert_init' argument 4 names different: declaration 'str' definition 'format_str'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/convert.h:41:81: note: Function 'convert_init' argument 4 names different: declaration 'str' definition 'format_str'.
pysam-0.23.0/bcftools/convert.c:1506:81: note: Function 'convert_init' argument 4 names different: declaration 'str' definition 'format_str'.
pysam-0.23.0/bcftools/convert.c:1653:46: style:inconclusive: Function 'convert_line' argument 2 names different: declaration 'rec' definition 'line'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/convert.h:45:46: note: Function 'convert_line' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/convert.c:1653:46: note: Function 'convert_line' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/convert.c:337:24: style: Local variable 'fmt' shadows outer argument [shadowArgument]
pysam-0.23.0/bcftools/convert.c:329:78: note: Shadowed declaration
pysam-0.23.0/bcftools/convert.c:337:24: note: Shadow variable
pysam-0.23.0/bcftools/convert.c:127:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'process_pos' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c:1308:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c:127:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c:129:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'process_end' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c:1310:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c:129:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c:130:54: style: Parameter 'line' can be declared as pointer to const. However it seems that 'process_end0' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c:1311:38: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c:130:54: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c:133:66: style: Parameter 'fmt' can be declared as pointer to const. However it seems that 'process_alt' is a callback function, if 'fmt' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c:1314:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c:133:66: note: Parameter 'fmt' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c:216:67: style: Parameter 'fmt' can be declared as pointer to const. However it seems that 'process_info' is a callback function, if 'fmt' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c:1317:38: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c:216:67: note: Parameter 'fmt' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c:440:13: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c:604:13: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c:747:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c:1126:47: style: Parameter 'convert' can be declared as pointer to const. However it seems that 'process_variantkey_hex' is a callback function, if 'convert' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c:1332:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c:1126:47: note: Parameter 'convert' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c:1146:38: style: Parameter 'convert' can be declared as pointer to const. However it seems that 'process_npass' is a callback function, if 'convert' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c:1334:39: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c:1146:38: note: Parameter 'convert' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c:1506:46: style: Parameter 'samples' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/convert.c:1742:15: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c:1800:35: style: Parameter 'convert' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/convert.c:653:85: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/convert.c.pysam.c:128:130: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:177:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:184:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_INT8 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:230:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:317:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:343:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:392:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_FLOAT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:439:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_INT8 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:601:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_BT_INT8 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:641:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_SNP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:649:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_REF [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:672:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:692:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:743:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:792:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:844:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:998:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:1125:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIx32 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:1138:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:1172:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:1274:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:1390:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:1513:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:1662:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/convert.c.pysam.c:203:16: style: Array index 'ibeg' is used before limits check. [arrayIndexThenCheck]
pysam-0.23.0/bcftools/convert.c.pysam.c:1511:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c.pysam.c:1511:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c.pysam.c:1512:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c.pysam.c:1512:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c.pysam.c:1513:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c.pysam.c:1513:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c.pysam.c:1514:5: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c.pysam.c:1514:5: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c.pysam.c:1517:15: warning: If memory allocation fails, then there is a possible null pointer dereference: convert [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/convert.c.pysam.c:1510:26: note: Assignment 'convert=(struct convert_t*)calloc(1,sizeof(struct convert_t))', assigned value is 0
pysam-0.23.0/bcftools/convert.c.pysam.c:1517:15: note: Null pointer dereference
pysam-0.23.0/bcftools/convert.c.pysam.c:1508:81: style:inconclusive: Function 'convert_init' argument 4 names different: declaration 'str' definition 'format_str'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/convert.h:41:81: note: Function 'convert_init' argument 4 names different: declaration 'str' definition 'format_str'.
pysam-0.23.0/bcftools/convert.c.pysam.c:1508:81: note: Function 'convert_init' argument 4 names different: declaration 'str' definition 'format_str'.
pysam-0.23.0/bcftools/convert.c.pysam.c:1655:46: style:inconclusive: Function 'convert_line' argument 2 names different: declaration 'rec' definition 'line'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/convert.h:45:46: note: Function 'convert_line' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/convert.c.pysam.c:1655:46: note: Function 'convert_line' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/convert.c.pysam.c:339:24: style: Local variable 'fmt' shadows outer argument [shadowArgument]
pysam-0.23.0/bcftools/convert.c.pysam.c:331:78: note: Shadowed declaration
pysam-0.23.0/bcftools/convert.c.pysam.c:339:24: note: Shadow variable
pysam-0.23.0/bcftools/convert.c.pysam.c:129:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'process_pos' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c.pysam.c:1310:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c.pysam.c:129:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c.pysam.c:131:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'process_end' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c.pysam.c:1312:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c.pysam.c:131:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c.pysam.c:132:54: style: Parameter 'line' can be declared as pointer to const. However it seems that 'process_end0' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c.pysam.c:1313:38: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c.pysam.c:132:54: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c.pysam.c:135:66: style: Parameter 'fmt' can be declared as pointer to const. However it seems that 'process_alt' is a callback function, if 'fmt' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c.pysam.c:1316:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c.pysam.c:135:66: note: Parameter 'fmt' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c.pysam.c:218:67: style: Parameter 'fmt' can be declared as pointer to const. However it seems that 'process_info' is a callback function, if 'fmt' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c.pysam.c:1319:38: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c.pysam.c:218:67: note: Parameter 'fmt' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c.pysam.c:442:13: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c.pysam.c:606:13: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c.pysam.c:749:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c.pysam.c:1128:47: style: Parameter 'convert' can be declared as pointer to const. However it seems that 'process_variantkey_hex' is a callback function, if 'convert' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c.pysam.c:1334:37: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c.pysam.c:1128:47: note: Parameter 'convert' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c.pysam.c:1148:38: style: Parameter 'convert' can be declared as pointer to const. However it seems that 'process_npass' is a callback function, if 'convert' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/convert.c.pysam.c:1336:39: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/convert.c.pysam.c:1148:38: note: Parameter 'convert' can be declared as pointer to const
pysam-0.23.0/bcftools/convert.c.pysam.c:1508:46: style: Parameter 'samples' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/convert.c.pysam.c:1744:15: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/convert.c.pysam.c:1802:35: style: Parameter 'convert' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/convert.c.pysam.c:655:85: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/csq.c:304:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/csq.c.pysam.c:306:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/dist.c:48:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c:47:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c:47:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c:48:5: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c:49:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c:47:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c:47:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c:49:5: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c:50:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c:47:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c:47:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c:50:5: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c:50:20: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c:47:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c:47:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c:50:20: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c:61:24: style: Parameter 'dist' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/dist.c:66:26: style: Parameter 'dist' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/dist.c.pysam.c:50:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c.pysam.c:49:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c.pysam.c:49:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c.pysam.c:50:5: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c.pysam.c:51:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c.pysam.c:49:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c.pysam.c:49:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c.pysam.c:51:5: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c.pysam.c:52:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c.pysam.c:49:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c.pysam.c:49:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c.pysam.c:52:5: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c.pysam.c:52:20: warning: If memory allocation fails, then there is a possible null pointer dereference: dist [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/dist.c.pysam.c:49:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/dist.c.pysam.c:49:20: note: Assignment 'dist=(struct dist_t*)calloc(1,sizeof(struct dist_t))', assigned value is 0
pysam-0.23.0/bcftools/dist.c.pysam.c:52:20: note: Null pointer dereference
pysam-0.23.0/bcftools/dist.c.pysam.c:63:24: style: Parameter 'dist' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/dist.c.pysam.c:68:26: style: Parameter 'dist' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/edlib.c:478:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/edlib.c:47:6: warning: If memory allocation fails, then there is a possible null pointer dereference: ed [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c:43:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c:43:36: note: Assignment 'ed=malloc(sizeof(*ed))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c:47:6: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c:270:13: warning: If memory allocation fails, then there is a possible null pointer dereference: Peq [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c:257:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c:257:23: note: Assignment 'Peq=malloc((alphabetLength+1)*maxNumBlocks*sizeof(*Peq))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c:270:13: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c:277:13: warning: If memory allocation fails, then there is a possible null pointer dereference: Peq [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c:257:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c:257:23: note: Assignment 'Peq=malloc((alphabetLength+1)*maxNumBlocks*sizeof(*Peq))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c:277:13: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c:292:9: warning: If memory allocation fails, then there is a possible null pointer dereference: rSeq [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c:290:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c:290:33: note: Assignment 'rSeq=malloc(length)', assigned value is 0
pysam-0.23.0/bcftools/edlib.c:292:9: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c:369:9: warning: If memory allocation fails, then there is a possible null pointer dereference: scores [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c:365:25: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c:365:25: note: Assignment 'scores=malloc(WORD_SIZE*sizeof(*scores))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c:369:9: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c:374:5: warning: If memory allocation fails, then there is a possible null pointer dereference: scores [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c:365:25: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c:365:25: note: Assignment 'scores=malloc(WORD_SIZE*sizeof(*scores))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c:374:5: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c:100:47: style:inconclusive: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/edlib.h:243:21: note: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'.
pysam-0.23.0/bcftools/edlib.c:100:47: note: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'.
pysam-0.23.0/bcftools/edlib.c:101:26: style:inconclusive: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/edlib.h:244:21: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
pysam-0.23.0/bcftools/edlib.c:101:26: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
pysam-0.23.0/bcftools/edlib.c:352:18: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/edlib.c:16:39: error: Shifting signed 64-bit value by 63 bits is undefined behaviour [shiftTooManyBitsSigned]
pysam-0.23.0/bcftools/edlib.c:499:37: style: Variable 'Peq_c' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/edlib.c.pysam.c:480:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/edlib.c.pysam.c:49:6: warning: If memory allocation fails, then there is a possible null pointer dereference: ed [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c.pysam.c:45:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c.pysam.c:45:36: note: Assignment 'ed=malloc(sizeof(*ed))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c.pysam.c:49:6: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c.pysam.c:272:13: warning: If memory allocation fails, then there is a possible null pointer dereference: Peq [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c.pysam.c:259:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c.pysam.c:259:23: note: Assignment 'Peq=malloc((alphabetLength+1)*maxNumBlocks*sizeof(*Peq))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c.pysam.c:272:13: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c.pysam.c:279:13: warning: If memory allocation fails, then there is a possible null pointer dereference: Peq [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c.pysam.c:259:23: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c.pysam.c:259:23: note: Assignment 'Peq=malloc((alphabetLength+1)*maxNumBlocks*sizeof(*Peq))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c.pysam.c:279:13: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c.pysam.c:294:9: warning: If memory allocation fails, then there is a possible null pointer dereference: rSeq [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c.pysam.c:292:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c.pysam.c:292:33: note: Assignment 'rSeq=malloc(length)', assigned value is 0
pysam-0.23.0/bcftools/edlib.c.pysam.c:294:9: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c.pysam.c:371:9: warning: If memory allocation fails, then there is a possible null pointer dereference: scores [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c.pysam.c:367:25: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c.pysam.c:367:25: note: Assignment 'scores=malloc(WORD_SIZE*sizeof(*scores))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c.pysam.c:371:9: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c.pysam.c:376:5: warning: If memory allocation fails, then there is a possible null pointer dereference: scores [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/edlib.c.pysam.c:367:25: note: Assuming allocation function fails
pysam-0.23.0/bcftools/edlib.c.pysam.c:367:25: note: Assignment 'scores=malloc(WORD_SIZE*sizeof(*scores))', assigned value is 0
pysam-0.23.0/bcftools/edlib.c.pysam.c:376:5: note: Null pointer dereference
pysam-0.23.0/bcftools/edlib.c.pysam.c:102:47: style:inconclusive: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/edlib.h:243:21: note: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'.
pysam-0.23.0/bcftools/edlib.c.pysam.c:102:47: note: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'.
pysam-0.23.0/bcftools/edlib.c.pysam.c:103:26: style:inconclusive: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/edlib.h:244:21: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
pysam-0.23.0/bcftools/edlib.c.pysam.c:103:26: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
pysam-0.23.0/bcftools/edlib.c.pysam.c:354:18: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/edlib.c.pysam.c:18:39: error: Shifting signed 64-bit value by 63 bits is undefined behaviour [shiftTooManyBitsSigned]
pysam-0.23.0/bcftools/edlib.c.pysam.c:501:37: style: Variable 'Peq_c' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/em.c:72:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/em.c:144:70: style: Parameter 'f3' can be declared as const array [constParameter]
pysam-0.23.0/bcftools/em.c:193:21: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/em.c.pysam.c:74:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/em.c.pysam.c:146:70: style: Parameter 'f3' can be declared as const array [constParameter]
pysam-0.23.0/bcftools/em.c.pysam.c:195:21: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/extsort.c:156:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRUSR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/extsort.c:90:5: warning: If memory allocation fails, then there is a possible null pointer dereference: es [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:89:40: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:89:21: note: Assignment 'es=(struct extsort_t*)calloc(1,sizeof(*es))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:90:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:135:5: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c:135:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:136:5: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c:136:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:137:5: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c:137:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:154:15: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c:154:15: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:154:33: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c:154:33: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:156:21: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c:156:21: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:157:16: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c:157:16: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:165:24: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c:133:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c:133:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:134:25: note: Assignment 'blk=es->blk[es->nblk-1]', assigned value is 0
pysam-0.23.0/bcftools/extsort.c:165:24: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c:80:26: style: Checking if unsigned expression 'es->max_mem' is less than zero. [unsignedLessThanZero]
pysam-0.23.0/bcftools/extsort.c.pysam.c:158:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRUSR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/extsort.c.pysam.c:92:5: warning: If memory allocation fails, then there is a possible null pointer dereference: es [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:91:40: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:91:21: note: Assignment 'es=(struct extsort_t*)calloc(1,sizeof(*es))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:92:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:137:5: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c.pysam.c:137:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:138:5: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c.pysam.c:138:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:139:5: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c.pysam.c:139:5: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:156:15: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c.pysam.c:156:15: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:156:33: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c.pysam.c:156:33: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:158:21: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c.pysam.c:158:21: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:159:16: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:16: note: blk is assigned 'es->blk[es->nblk-1]' here.
pysam-0.23.0/bcftools/extsort.c.pysam.c:159:16: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:167:24: warning: If memory allocation fails, then there is a possible null pointer dereference: blk [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/extsort.c.pysam.c:135:27: note: Assignment 'es->blk[es->nblk-1]=(struct blk_t*)calloc(1,sizeof(struct blk_t))', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:136:25: note: Assignment 'blk=es->blk[es->nblk-1]', assigned value is 0
pysam-0.23.0/bcftools/extsort.c.pysam.c:167:24: note: Null pointer dereference
pysam-0.23.0/bcftools/extsort.c.pysam.c:82:26: style: Checking if unsigned expression 'es->max_mem' is less than zero. [unsignedLessThanZero]
pysam-0.23.0/bcftools/filter.c:446:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:487:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:773:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:951:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:959:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1044:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1135:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1262:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1373:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1442:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1512:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1560:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1579:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:1627:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:2091:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:2860:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:2946:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:2966:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:2992:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:3340:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:3493:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:3512:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:3933:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:3976:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:4008:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c:406:38: portability: Non reentrant function 'getpwnam' called. For threadsafe applications it is recommended to use the reentrant replacement function 'getpwnam_r'. [prohibitedgetpwnamCalled]
pysam-0.23.0/bcftools/filter.c:744:32: warning: Either the condition '!regex' is redundant or there is possible null pointer dereference: regex. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/filter.c:743:22: note: Assuming that condition '!regex' is not redundant
pysam-0.23.0/bcftools/filter.c:744:32: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c:2767:10: warning: If memory allocation fails, then there is a possible null pointer dereference: *idxs [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/filter.c:2766:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/filter.c:2766:17: note: Assignment '*idxs=(int*)malloc(sizeof(int))', assigned value is 0
pysam-0.23.0/bcftools/filter.c:2767:10: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c:2775:10: warning: If memory allocation fails, then there is a possible null pointer dereference: *idxs [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/filter.c:2774:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/filter.c:2774:17: note: Assignment '*idxs=(int*)malloc(sizeof(int))', assigned value is 0
pysam-0.23.0/bcftools/filter.c:2775:10: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c:3336:42: warning: Possible null pointer dereference: tok_ptrs [nullPointer]
pysam-0.23.0/bcftools/filter.c:3909:36: note: Calling function 'filter_debug_print', 2nd argument 'NULL' value is 0
pysam-0.23.0/bcftools/filter.c:3336:42: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c:754:33: style: Same expression on both sides of '||'. [duplicateExpression]
pysam-0.23.0/bcftools/filter.c:800:116: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c:801:116: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c:802:116: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c:803:123: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c:343:60: style:inconclusive: Function 'filter_list_undef_tags' argument 2 names different: declaration 'nundef' definition 'ntags'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:103:60: note: Function 'filter_list_undef_tags' argument 2 names different: declaration 'nundef' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c:343:60: note: Function 'filter_list_undef_tags' argument 2 names different: declaration 'nundef' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c:368:59: style:inconclusive: Function 'filter_list_used_tags' argument 2 names different: declaration 'nused' definition 'ntags'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:104:59: note: Function 'filter_list_used_tags' argument 2 names different: declaration 'nused' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c:368:59: note: Function 'filter_list_used_tags' argument 2 names different: declaration 'nused' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c:3993:43: style:inconclusive: Function 'filter_test' argument 2 names different: declaration 'rec' definition 'line'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:50:43: note: Function 'filter_test' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/filter.c:3993:43: note: Function 'filter_test' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/filter.c:4125:33: style:inconclusive: Function 'filter_max_unpack' argument 1 names different: declaration 'filter' definition 'flt'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:80:33: note: Function 'filter_max_unpack' argument 1 names different: declaration 'filter' definition 'flt'.
pysam-0.23.0/bcftools/filter.c:4125:33: note: Function 'filter_max_unpack' argument 1 names different: declaration 'filter' definition 'flt'.
pysam-0.23.0/bcftools/filter.c:3853:22: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/filter.c:3519:11: note: Shadowed declaration
pysam-0.23.0/bcftools/filter.c:3853:22: note: Shadow variable
pysam-0.23.0/bcftools/filter.c:532:31: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c:534:31: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c:3878:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c:4115:50: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c:331:58: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:536:56: style: Parameter 'btok' can be declared as pointer to const. However it seems that 'filters_cmp_filter' is a callback function, if 'btok' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3047:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:536:56: note: Parameter 'btok' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:536:85: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_cmp_filter' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3047:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:536:85: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:742:26: style: Variable 'regex' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:818:52: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_pos' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3073:28: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:818:52: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:947:58: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_info_flag' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3204:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:947:58: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:977:22: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:996:22: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1014:22: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1313:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_ilen' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3296:24: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:1313:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:1434:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_nalt' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3103:28: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:1434:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:1512:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1556:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1579:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1623:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1646:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1686:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1871:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1911:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1931:14: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1970:14: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:1979:21: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2100:25: style: Variable 'vals' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2123:25: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2124:25: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2145:17: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2145:31: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2219:14: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2613:43: style: Parameter 'regex' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:2613:89: style: Parameter 'missing_logic' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:2615:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2647:107: style: Parameter 'missing_logic' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:2649:11: style: Variable 'aend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2650:11: style: Variable 'bend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2782:17: style: Variable 'beg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:2956:54: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:3336:18: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:3357:32: style: Parameter 'flt' can be declared as pointer to const. However it seems that 'perl_exec' is a callback function, if 'flt' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3893:66: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:3357:32: note: Parameter 'flt' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:3357:45: style: Parameter 'line' can be declared as pointer to const. However it seems that 'perl_exec' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3893:66: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:3357:45: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:3357:60: style: Parameter 'rtok' can be declared as pointer to const. However it seems that 'perl_exec' is a callback function, if 'rtok' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c:3893:66: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c:3357:60: note: Parameter 'rtok' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c:3417:33: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:3419:11: style: Variable 'beg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c:3462:36: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:4125:33: style: Parameter 'flt' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:4129:39: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:4162:29: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c:460:40: warning: Shifting 32-bit value by 63 bits is undefined behaviour. See condition at line 448. [shiftTooManyBits]
pysam-0.23.0/bcftools/filter.c:448:25: note: Assuming that condition 'allele>63' is not redundant
pysam-0.23.0/bcftools/filter.c:460:40: note: Shift
pysam-0.23.0/bcftools/filter.c.pysam.c:448:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:489:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:775:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:953:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:961:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1046:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1137:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1264:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1375:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1444:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1514:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1562:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1581:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:1629:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:2093:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:2862:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:2948:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:2968:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:2994:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:3495:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:3514:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:3935:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:3978:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:4010:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/filter.c.pysam.c:408:38: portability: Non reentrant function 'getpwnam' called. For threadsafe applications it is recommended to use the reentrant replacement function 'getpwnam_r'. [prohibitedgetpwnamCalled]
pysam-0.23.0/bcftools/filter.c.pysam.c:746:32: warning: Either the condition '!regex' is redundant or there is possible null pointer dereference: regex. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/filter.c.pysam.c:745:22: note: Assuming that condition '!regex' is not redundant
pysam-0.23.0/bcftools/filter.c.pysam.c:746:32: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c.pysam.c:2769:10: warning: If memory allocation fails, then there is a possible null pointer dereference: *idxs [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/filter.c.pysam.c:2768:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/filter.c.pysam.c:2768:17: note: Assignment '*idxs=(int*)malloc(sizeof(int))', assigned value is 0
pysam-0.23.0/bcftools/filter.c.pysam.c:2769:10: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c.pysam.c:2777:10: warning: If memory allocation fails, then there is a possible null pointer dereference: *idxs [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/filter.c.pysam.c:2776:30: note: Assuming allocation function fails
pysam-0.23.0/bcftools/filter.c.pysam.c:2776:17: note: Assignment '*idxs=(int*)malloc(sizeof(int))', assigned value is 0
pysam-0.23.0/bcftools/filter.c.pysam.c:2777:10: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c.pysam.c:3338:42: warning: Possible null pointer dereference: tok_ptrs [nullPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:3911:36: note: Calling function 'filter_debug_print', 2nd argument 'NULL' value is 0
pysam-0.23.0/bcftools/filter.c.pysam.c:3338:42: note: Null pointer dereference
pysam-0.23.0/bcftools/filter.c.pysam.c:756:33: style: Same expression on both sides of '||'. [duplicateExpression]
pysam-0.23.0/bcftools/filter.c.pysam.c:802:116: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c.pysam.c:803:116: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c.pysam.c:804:116: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c.pysam.c:805:123: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/filter.c.pysam.c:345:60: style:inconclusive: Function 'filter_list_undef_tags' argument 2 names different: declaration 'nundef' definition 'ntags'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:103:60: note: Function 'filter_list_undef_tags' argument 2 names different: declaration 'nundef' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c.pysam.c:345:60: note: Function 'filter_list_undef_tags' argument 2 names different: declaration 'nundef' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c.pysam.c:370:59: style:inconclusive: Function 'filter_list_used_tags' argument 2 names different: declaration 'nused' definition 'ntags'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:104:59: note: Function 'filter_list_used_tags' argument 2 names different: declaration 'nused' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c.pysam.c:370:59: note: Function 'filter_list_used_tags' argument 2 names different: declaration 'nused' definition 'ntags'.
pysam-0.23.0/bcftools/filter.c.pysam.c:3995:43: style:inconclusive: Function 'filter_test' argument 2 names different: declaration 'rec' definition 'line'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:50:43: note: Function 'filter_test' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/filter.c.pysam.c:3995:43: note: Function 'filter_test' argument 2 names different: declaration 'rec' definition 'line'.
pysam-0.23.0/bcftools/filter.c.pysam.c:4127:33: style:inconclusive: Function 'filter_max_unpack' argument 1 names different: declaration 'filter' definition 'flt'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/filter.h:80:33: note: Function 'filter_max_unpack' argument 1 names different: declaration 'filter' definition 'flt'.
pysam-0.23.0/bcftools/filter.c.pysam.c:4127:33: note: Function 'filter_max_unpack' argument 1 names different: declaration 'filter' definition 'flt'.
pysam-0.23.0/bcftools/filter.c.pysam.c:3855:22: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/filter.c.pysam.c:3521:11: note: Shadowed declaration
pysam-0.23.0/bcftools/filter.c.pysam.c:3855:22: note: Shadow variable
pysam-0.23.0/bcftools/filter.c.pysam.c:534:31: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c.pysam.c:536:31: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c.pysam.c:3880:54: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c.pysam.c:4117:50: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/filter.c.pysam.c:333:58: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:538:56: style: Parameter 'btok' can be declared as pointer to const. However it seems that 'filters_cmp_filter' is a callback function, if 'btok' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3049:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:538:56: note: Parameter 'btok' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:538:85: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_cmp_filter' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3049:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:538:85: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:744:26: style: Variable 'regex' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:820:52: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_pos' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3075:28: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:820:52: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:949:58: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_info_flag' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3206:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:949:58: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:979:22: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:998:22: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1016:22: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1315:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_ilen' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3298:24: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:1315:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:1436:53: style: Parameter 'line' can be declared as pointer to const. However it seems that 'filters_set_nalt' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3105:28: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:1436:53: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:1514:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1558:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1581:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1625:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1648:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1688:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1873:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1913:18: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1933:14: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1972:14: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:1981:21: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2102:25: style: Variable 'vals' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2125:25: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2126:25: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2147:17: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2147:31: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2221:14: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2615:43: style: Parameter 'regex' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2615:89: style: Parameter 'missing_logic' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2617:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2649:107: style: Parameter 'missing_logic' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2651:11: style: Variable 'aend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2652:11: style: Variable 'bend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2784:17: style: Variable 'beg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:2958:54: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:3338:18: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:3359:32: style: Parameter 'flt' can be declared as pointer to const. However it seems that 'perl_exec' is a callback function, if 'flt' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3895:66: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:3359:32: note: Parameter 'flt' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:3359:45: style: Parameter 'line' can be declared as pointer to const. However it seems that 'perl_exec' is a callback function, if 'line' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3895:66: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:3359:45: note: Parameter 'line' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:3359:60: style: Parameter 'rtok' can be declared as pointer to const. However it seems that 'perl_exec' is a callback function, if 'rtok' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/filter.c.pysam.c:3895:66: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/filter.c.pysam.c:3359:60: note: Parameter 'rtok' can be declared as pointer to const
pysam-0.23.0/bcftools/filter.c.pysam.c:3419:33: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:3421:11: style: Variable 'beg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:3464:36: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:4127:33: style: Parameter 'flt' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:4131:39: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:4164:29: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/filter.c.pysam.c:462:40: warning: Shifting 32-bit value by 63 bits is undefined behaviour. See condition at line 450. [shiftTooManyBits]
pysam-0.23.0/bcftools/filter.c.pysam.c:450:25: note: Assuming that condition 'allele>63' is not redundant
pysam-0.23.0/bcftools/filter.c.pysam.c:462:40: note: Shift
pysam-0.23.0/bcftools/gff.c:49:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/gff.c.pysam.c:51:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/gvcf.c:104:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/gvcf.c:49:5: warning: If memory allocation fails, then there is a possible null pointer dereference: gvcf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/gvcf.c:48:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/gvcf.c:48:20: note: Assignment 'gvcf=(struct gvcf_t*)calloc(1,sizeof(struct gvcf_t))', assigned value is 0
pysam-0.23.0/bcftools/gvcf.c:49:5: note: Null pointer dereference
pysam-0.23.0/bcftools/gvcf.c.pysam.c:106:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/gvcf.c.pysam.c:51:5: warning: If memory allocation fails, then there is a possible null pointer dereference: gvcf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/gvcf.c.pysam.c:50:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/gvcf.c.pysam.c:50:20: note: Assignment 'gvcf=(struct gvcf_t*)calloc(1,sizeof(struct gvcf_t))', assigned value is 0
pysam-0.23.0/bcftools/gvcf.c.pysam.c:51:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:141:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/hclust.c:319:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/hclust.c:215:43: style: Condition 'node->akid' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/hclust.c:223:43: style: Condition 'node->bkid' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/hclust.c:58:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c:58:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:59:5: warning: If memory allocation fails, then there is a possible null pointer dereference: node [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:56:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:56:20: note: Assignment 'node=(struct node_t*)calloc(1,sizeof(struct node_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:59:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:59:17: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c:59:17: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:60:5: warning: If memory allocation fails, then there is a possible null pointer dereference: node [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:56:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:56:20: note: Assignment 'node=(struct node_t*)calloc(1,sizeof(struct node_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:60:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:61:11: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c:61:11: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:73:10: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c:73:10: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:73:26: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c:73:26: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:74:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c:74:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:74:17: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c:74:17: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:129:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:129:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:130:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:130:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:131:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:131:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:135:17: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:17: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:138:13: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:138:13: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:142:26: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:142:26: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:146:30: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:146:30: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:149:31: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:149:31: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:352:5: warning: If memory allocation fails, then there is a possible null pointer dereference: stack [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:350:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:350:22: note: Assignment 'stack=(struct node_t**)malloc(sizeof(struct node_t*)*clust->ndat)', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:352:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:358:10: warning: If memory allocation fails, then there is a possible null pointer dereference: stack [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:350:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:350:22: note: Assignment 'stack=(struct node_t**)malloc(sizeof(struct node_t*)*clust->ndat)', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:358:10: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:367:24: warning: If memory allocation fails, then there is a possible null pointer dereference: stack [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:350:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:350:22: note: Assignment 'stack=(struct node_t**)malloc(sizeof(struct node_t*)*clust->ndat)', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:367:24: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c:266:17: style: Local variable 'node' shadows outer argument [shadowArgument]
pysam-0.23.0/bcftools/hclust.c:252:35: note: Shadowed declaration
pysam-0.23.0/bcftools/hclust.c:266:17: note: Shadow variable
pysam-0.23.0/bcftools/hclust.c:358:18: error: Memory is allocated but not initialized: stack[0]->value [uninitdata]
pysam-0.23.0/bcftools/hclust.c.pysam.c:143:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/hclust.c.pysam.c:321:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/hclust.c.pysam.c:217:43: style: Condition 'node->akid' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/hclust.c.pysam.c:225:43: style: Condition 'node->bkid' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/hclust.c.pysam.c:60:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:60:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:61:5: warning: If memory allocation fails, then there is a possible null pointer dereference: node [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:58:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:58:20: note: Assignment 'node=(struct node_t*)calloc(1,sizeof(struct node_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:61:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:61:17: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:61:17: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:62:5: warning: If memory allocation fails, then there is a possible null pointer dereference: node [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:58:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:58:20: note: Assignment 'node=(struct node_t*)calloc(1,sizeof(struct node_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:62:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:63:11: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:63:11: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:75:10: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:75:10: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:75:26: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:75:26: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:76:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:76:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:76:17: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:47: note: Calling function 'append_node', 1st argument 'clust' value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:76:17: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:131:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:131:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:132:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:132:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:133:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:133:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:17: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:17: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:140:13: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:140:13: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:144:26: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:144:26: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:148:30: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:148:30: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:151:31: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:151:31: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:354:5: warning: If memory allocation fails, then there is a possible null pointer dereference: stack [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:352:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:352:22: note: Assignment 'stack=(struct node_t**)malloc(sizeof(struct node_t*)*clust->ndat)', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:354:5: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:360:10: warning: If memory allocation fails, then there is a possible null pointer dereference: stack [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:352:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:352:22: note: Assignment 'stack=(struct node_t**)malloc(sizeof(struct node_t*)*clust->ndat)', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:360:10: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:369:24: warning: If memory allocation fails, then there is a possible null pointer dereference: stack [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:352:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:352:22: note: Assignment 'stack=(struct node_t**)malloc(sizeof(struct node_t*)*clust->ndat)', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:369:24: note: Null pointer dereference
pysam-0.23.0/bcftools/hclust.c.pysam.c:268:17: style: Local variable 'node' shadows outer argument [shadowArgument]
pysam-0.23.0/bcftools/hclust.c.pysam.c:254:35: note: Shadowed declaration
pysam-0.23.0/bcftools/hclust.c.pysam.c:268:17: note: Shadow variable
pysam-0.23.0/bcftools/hclust.c.pysam.c:360:18: error: Memory is allocated but not initialized: stack[0]->value [uninitdata]
pysam-0.23.0/bcftools/kmin.c:52:3: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: x1 [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c:71:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c:71:7: note: Assignment 'x1=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c:81:32: note: Calling function '__kmin_hj_aux', 3rd argument 'x1' value is 0
pysam-0.23.0/bcftools/kmin.c:52:3: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c:52:12: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c:72:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c:72:7: note: Assignment 'dx=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c:81:46: note: Calling function '__kmin_hj_aux', 6th argument 'dx' value is 0
pysam-0.23.0/bcftools/kmin.c:52:12: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c:74:3: warning: If memory allocation fails, then there is a possible null pointer dereference: dx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c:72:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c:72:7: note: Assignment 'dx=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c:74:3: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c:75:7: warning: If memory allocation fails, then there is a possible null pointer dereference: dx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c:72:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c:72:7: note: Assignment 'dx=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c:75:7: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c:80:10: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: x1 [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c:71:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c:71:7: note: Assignment 'x1=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c:80:10: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c:137:22: style: Variable 'fa' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/kmin.c:140:15: style: Variable 'fc' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/kmin.c:151:8: style: Variable 'fa' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/kmin.c:151:26: style: Variable 'fc' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/kmin.c.pysam.c:54:3: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: x1 [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c.pysam.c:73:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c.pysam.c:73:7: note: Assignment 'x1=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c.pysam.c:83:32: note: Calling function '__kmin_hj_aux', 3rd argument 'x1' value is 0
pysam-0.23.0/bcftools/kmin.c.pysam.c:54:3: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c.pysam.c:54:12: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c.pysam.c:74:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c.pysam.c:74:7: note: Assignment 'dx=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c.pysam.c:83:46: note: Calling function '__kmin_hj_aux', 6th argument 'dx' value is 0
pysam-0.23.0/bcftools/kmin.c.pysam.c:54:12: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c.pysam.c:76:3: warning: If memory allocation fails, then there is a possible null pointer dereference: dx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c.pysam.c:74:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c.pysam.c:74:7: note: Assignment 'dx=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c.pysam.c:76:3: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c.pysam.c:77:7: warning: If memory allocation fails, then there is a possible null pointer dereference: dx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c.pysam.c:74:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c.pysam.c:74:7: note: Assignment 'dx=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c.pysam.c:77:7: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c.pysam.c:82:10: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: x1 [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/kmin.c.pysam.c:73:22: note: Assuming allocation function fails
pysam-0.23.0/bcftools/kmin.c.pysam.c:73:7: note: Assignment 'x1=(double*)calloc(n,sizeof(double))', assigned value is 0
pysam-0.23.0/bcftools/kmin.c.pysam.c:82:10: note: Null pointer dereference
pysam-0.23.0/bcftools/kmin.c.pysam.c:139:22: style: Variable 'fa' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/kmin.c.pysam.c:142:15: style: Variable 'fc' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/kmin.c.pysam.c:153:8: style: Variable 'fa' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/kmin.c.pysam.c:153:26: style: Variable 'fc' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/main.c:205:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCFTOOLS_VERSION [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/main.c:265:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/main.c.pysam.c:207:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCFTOOLS_VERSION [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/main.c.pysam.c:309:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:115:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:268:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:412:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:465:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:595:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:731:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:769:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:1183:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:1209:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:1284:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:1480:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c:576:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/mcall.c:578:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/mcall.c:642:35: style: Condition 'call->ploidy' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/mcall.c:687:39: style: Condition 'call->ploidy' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/mcall.c:1424:89: style: Condition 'mcall_constrain_alleles(call,rec,&unseen)!=0' is always false [knownConditionTrueFalse]
pysam-0.23.0/bcftools/mcall.c:1424:69: note: Calling function 'mcall_constrain_alleles' returns 0
pysam-0.23.0/bcftools/mcall.c:1424:89: note: Condition 'mcall_constrain_alleles(call,rec,&unseen)!=0' is always false
pysam-0.23.0/bcftools/mcall.c:595:12: style:inconclusive: Same expression used in consecutive assignments of 'ref_lk' and 'max_lk'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c:595:32: note: Same expression used in consecutive assignments of 'ref_lk' and 'max_lk'.
pysam-0.23.0/bcftools/mcall.c:595:12: note: Same expression used in consecutive assignments of 'ref_lk' and 'max_lk'.
pysam-0.23.0/bcftools/mcall.c:595:32: style:inconclusive: Same expression used in consecutive assignments of 'max_lk' and 'lk_sum'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c:596:12: note: Same expression used in consecutive assignments of 'max_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c:595:32: note: Same expression used in consecutive assignments of 'max_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c:1536:12: style:inconclusive: Same expression used in consecutive assignments of 'ref_lk' and 'lk_sum'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c:1536:32: note: Same expression used in consecutive assignments of 'ref_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c:1536:12: note: Same expression used in consecutive assignments of 'ref_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c:1536:32: style:inconclusive: Same expression used in consecutive assignments of 'lk_sum' and 'max_qual'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c:1536:52: note: Same expression used in consecutive assignments of 'lk_sum' and 'max_qual'.
pysam-0.23.0/bcftools/mcall.c:1536:32: note: Same expression used in consecutive assignments of 'lk_sum' and 'max_qual'.
pysam-0.23.0/bcftools/mcall.c:1386:13: style: Local variable 'nsmpl' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/mcall.c:1334:9: note: Shadowed declaration
pysam-0.23.0/bcftools/mcall.c:1386:13: note: Shadow variable
pysam-0.23.0/bcftools/mcall.c:46:25: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c:47:28: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c:48:19: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c:48:33: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c:591:44: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c:609:21: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c:638:29: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c:683:33: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c:760:17: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c:1248:19: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c:1396:26: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c:1476:26: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:117:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:270:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:467:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:597:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:733:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:771:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1185:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1211:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1286:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1482:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mcall.c.pysam.c:578:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/mcall.c.pysam.c:580:16: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
pysam-0.23.0/bcftools/mcall.c.pysam.c:644:35: style: Condition 'call->ploidy' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/mcall.c.pysam.c:689:39: style: Condition 'call->ploidy' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1426:89: style: Condition 'mcall_constrain_alleles(call,rec,&unseen)!=0' is always false [knownConditionTrueFalse]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1426:69: note: Calling function 'mcall_constrain_alleles' returns 0
pysam-0.23.0/bcftools/mcall.c.pysam.c:1426:89: note: Condition 'mcall_constrain_alleles(call,rec,&unseen)!=0' is always false
pysam-0.23.0/bcftools/mcall.c.pysam.c:597:12: style:inconclusive: Same expression used in consecutive assignments of 'ref_lk' and 'max_lk'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c.pysam.c:597:32: note: Same expression used in consecutive assignments of 'ref_lk' and 'max_lk'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:597:12: note: Same expression used in consecutive assignments of 'ref_lk' and 'max_lk'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:597:32: style:inconclusive: Same expression used in consecutive assignments of 'max_lk' and 'lk_sum'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c.pysam.c:598:12: note: Same expression used in consecutive assignments of 'max_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:597:32: note: Same expression used in consecutive assignments of 'max_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:1538:12: style:inconclusive: Same expression used in consecutive assignments of 'ref_lk' and 'lk_sum'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1538:32: note: Same expression used in consecutive assignments of 'ref_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:1538:12: note: Same expression used in consecutive assignments of 'ref_lk' and 'lk_sum'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:1538:32: style:inconclusive: Same expression used in consecutive assignments of 'lk_sum' and 'max_qual'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1538:52: note: Same expression used in consecutive assignments of 'lk_sum' and 'max_qual'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:1538:32: note: Same expression used in consecutive assignments of 'lk_sum' and 'max_qual'.
pysam-0.23.0/bcftools/mcall.c.pysam.c:1388:13: style: Local variable 'nsmpl' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1336:9: note: Shadowed declaration
pysam-0.23.0/bcftools/mcall.c.pysam.c:1388:13: note: Shadow variable
pysam-0.23.0/bcftools/mcall.c.pysam.c:48:25: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:49:28: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:50:19: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:50:33: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:593:44: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:611:21: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:640:29: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:685:33: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:762:17: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1250:19: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1398:26: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mcall.c.pysam.c:1478:26: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mpileup.c:207:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:309:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nm [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:370:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:385:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:433:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:579:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_table [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:621:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:1058:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:1131:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:1374:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c:1087:9: error: Common realloc mistake: 'files' nulled but not freed upon failure [memleakOnRealloc]
pysam-0.23.0/bcftools/mpileup.c:266:24: warning: If memory allocation fails, then there is a possible null pointer dereference: ZQ [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/mpileup.c:265:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/mpileup.c:265:37: note: Assignment 'ZQ=malloc((uint32_t)b->core.l_qseq+1)', assigned value is 0
pysam-0.23.0/bcftools/mpileup.c:266:24: note: Null pointer dereference
pysam-0.23.0/bcftools/mpileup.c:267:17: warning: If memory allocation fails, then there is a possible null pointer dereference: ZQ [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/mpileup.c:265:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/mpileup.c:265:37: note: Assignment 'ZQ=malloc((uint32_t)b->core.l_qseq+1)', assigned value is 0
pysam-0.23.0/bcftools/mpileup.c:267:17: note: Null pointer dereference
pysam-0.23.0/bcftools/mpileup.c:327:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/mpileup.c:317:9: note: Shadowed declaration
pysam-0.23.0/bcftools/mpileup.c:327:13: note: Shadow variable
pysam-0.23.0/bcftools/mpileup.c:330:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mpileup.c:361:73: style: Parameter 'n_plp' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mpileup.c:1130:15: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:209:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:311:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nm [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:372:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:387:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:435:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:581:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_table [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:623:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:1060:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:1376:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:1089:9: error: Common realloc mistake: 'files' nulled but not freed upon failure [memleakOnRealloc]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:268:24: warning: If memory allocation fails, then there is a possible null pointer dereference: ZQ [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:267:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/mpileup.c.pysam.c:267:37: note: Assignment 'ZQ=malloc((uint32_t)b->core.l_qseq+1)', assigned value is 0
pysam-0.23.0/bcftools/mpileup.c.pysam.c:268:24: note: Null pointer dereference
pysam-0.23.0/bcftools/mpileup.c.pysam.c:269:17: warning: If memory allocation fails, then there is a possible null pointer dereference: ZQ [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:267:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/mpileup.c.pysam.c:267:37: note: Assignment 'ZQ=malloc((uint32_t)b->core.l_qseq+1)', assigned value is 0
pysam-0.23.0/bcftools/mpileup.c.pysam.c:269:17: note: Null pointer dereference
pysam-0.23.0/bcftools/mpileup.c.pysam.c:329:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:319:9: note: Shadowed declaration
pysam-0.23.0/bcftools/mpileup.c.pysam.c:329:13: note: Shadow variable
pysam-0.23.0/bcftools/mpileup.c.pysam.c:332:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:363:73: style: Parameter 'n_plp' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/mpileup.c.pysam.c:1132:15: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/ploidy.c:213:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sex [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ploidy.c:50:36: style: Parameter 'ploidy' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ploidy.c:192:42: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ploidy.c:229:27: style: Parameter 'ploidy' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ploidy.c.pysam.c:215:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sex [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/ploidy.c.pysam.c:52:36: style: Parameter 'ploidy' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ploidy.c.pysam.c:194:42: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/ploidy.c.pysam.c:231:27: style: Parameter 'ploidy' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/prob1.c:122:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/prob1.c:519:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/prob1.c:66:29: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:112:23: note: Calling function 'bcf_p1_init_prior', 1st argument 'ma' value is 0
pysam-0.23.0/bcftools/prob1.c:66:29: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:66:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:112:23: note: Calling function 'bcf_p1_init_prior', 1st argument 'ma' value is 0
pysam-0.23.0/bcftools/prob1.c:66:36: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:84:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:84:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:85:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:85:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:86:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:86:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:88:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:88:9: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:89:16: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:89:16: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:90:21: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:90:21: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:90:49: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:90:49: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:91:13: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:91:13: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:96:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:96:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:97:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:97:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:97:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:97:36: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:98:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:98:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:98:32: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:98:32: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:99:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:99:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:99:38: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:99:38: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:100:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:100:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:100:33: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:100:33: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:101:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:101:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:101:33: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:101:33: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:102:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:102:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:102:30: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:102:30: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:103:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:103:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:103:34: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:103:34: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:104:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:104:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:104:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:104:31: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:105:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:105:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:105:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:105:31: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:106:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:106:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:106:32: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:106:32: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:107:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:107:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:107:33: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:107:33: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:108:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:108:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:108:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:108:31: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:110:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:110:9: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:111:22: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:111:22: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:111:34: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:111:34: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:156:12: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:155:27: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:155:13: note: Assignment 'p=(long*)malloc(b->n_allele*sizeof(long))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:156:12: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c:79:47: style: Parameter 'ploidy' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/prob1.c:116:31: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/prob1.c:184:25: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/prob1.c:214:26: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/prob1.c:427:13: style: Variable 'phi' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/prob1.c:453:24: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/prob1.c:219:9: style: Variable 'pdg' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c:387:38: style: Variable 'L[0]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c:387:45: style: Variable 'L[1]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c:412:48: style: Variable 'L[0]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c:412:55: style: Variable 'L[1]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c.pysam.c:124:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/prob1.c.pysam.c:68:29: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:114:23: note: Calling function 'bcf_p1_init_prior', 1st argument 'ma' value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:68:29: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:68:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:114:23: note: Calling function 'bcf_p1_init_prior', 1st argument 'ma' value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:68:36: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:86:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:86:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:87:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:87:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:88:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:88:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:90:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:90:9: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:91:16: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:91:16: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:92:21: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:92:21: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:92:49: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:92:49: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:93:13: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:93:13: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:98:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:98:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:99:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:99:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:99:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:99:36: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:100:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:100:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:100:32: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:100:32: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:101:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:101:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:101:38: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:101:38: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:102:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:102:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:102:33: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:102:33: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:103:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:103:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:103:33: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:103:33: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:104:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:104:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:104:30: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:104:30: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:105:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:105:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:105:34: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:105:34: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:106:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:106:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:106:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:106:31: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:107:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:107:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:107:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:107:31: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:108:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:108:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:108:32: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:108:32: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:109:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:109:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:109:33: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:109:33: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:110:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:110:5: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:110:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:110:31: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:112:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:112:9: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:113:22: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:113:22: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:113:34: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:113:34: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:158:12: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:157:27: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:157:13: note: Assignment 'p=(long*)malloc(b->n_allele*sizeof(long))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:158:12: note: Null pointer dereference
pysam-0.23.0/bcftools/prob1.c.pysam.c:81:47: style: Parameter 'ploidy' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/prob1.c.pysam.c:118:31: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/prob1.c.pysam.c:186:25: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/prob1.c.pysam.c:216:26: style: Variable 'pdg' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/prob1.c.pysam.c:429:13: style: Variable 'phi' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/prob1.c.pysam.c:455:24: style: Parameter 'call' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/prob1.c.pysam.c:221:9: style: Variable 'pdg' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c.pysam.c:389:38: style: Variable 'L[0]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c.pysam.c:389:45: style: Variable 'L[1]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c.pysam.c:414:48: style: Variable 'L[0]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/prob1.c.pysam.c:414:55: style: Variable 'L[1]' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/cigar_state.h:82:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/cigar_state.h:146:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c:167:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c:250:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c:520:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c:672:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c:698:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c:121:17: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:223:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c:121:17: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:121:29: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:223:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c:121:29: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:122:14: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:223:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c:122:14: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:141:12: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:223:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c:141:12: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:142:12: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:223:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c:142:12: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:148:12: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:223:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c:148:12: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:219:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:219:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:220:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:220:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:221:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:221:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:222:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:222:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c:70:55: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/read_consensus.c:70:75: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/read_consensus.c:245:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c:383:22: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c:384:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c:525:29: style: Variable 'ifrq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c:537:29: style: Variable 'dfrq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c:670:11: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c:758:19: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:169:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:252:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:522:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:674:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:700:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_nt16_int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:123:17: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:225:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:123:17: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:123:29: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:225:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:123:29: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:124:14: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:225:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:124:14: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:143:12: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:225:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:143:12: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:144:12: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:225:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:144:12: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:150:12: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:225:22: note: Calling function 'init_arrays', 1st argument 'rcns' value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:150:12: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:221:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:221:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:222:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:222:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:223:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:223:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:224:5: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:224:5: note: Null pointer dereference
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:72:55: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:72:75: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:247:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:385:22: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:386:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:527:29: style: Variable 'ifrq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:539:29: style: Variable 'dfrq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:672:11: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:760:19: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/regidx.c:259:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/regidx.c:456:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/regidx.c:488:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/regidx.c:534:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/regidx.c:407:68: style: Condition 'list->reg[ireg].beg<=end' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/regidx.c:406:38: note: Assuming that condition 'list->reg[ireg].beg>end' is not redundant
pysam-0.23.0/bcftools/regidx.c:407:68: note: Condition 'list->reg[ireg].beg<=end' is always true
pysam-0.23.0/bcftools/regidx.c:593:63: style: Condition 'list->reg[i].beg<=itr->end' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/regidx.c:592:31: note: Assuming that condition 'list->reg[i].beg>itr->end' is not redundant
pysam-0.23.0/bcftools/regidx.c:593:63: note: Condition 'list->reg[i].beg<=itr->end' is always true
pysam-0.23.0/bcftools/regidx.c:245:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:244:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:244:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:245:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:246:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:244:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:244:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:246:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:247:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:244:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:244:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:247:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:248:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:244:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:244:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:248:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:249:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:244:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:244:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:249:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:312:42: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:311:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:311:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:312:42: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:313:19: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:311:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:311:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:313:19: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:318:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:311:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:311:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:318:31: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:329:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:311:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:311:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:329:31: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:330:17: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_reg [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:326:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:326:30: note: Assignment 'tmp_reg=(struct reg_t*)malloc(sizeof(struct reg_t)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:330:17: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:554:5: warning: If memory allocation fails, then there is a possible null pointer dereference: regitr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:553:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:553:24: note: Assignment 'regitr=(struct regitr_t*)calloc(1,sizeof(struct regitr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:554:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:555:29: warning: If memory allocation fails, then there is a possible null pointer dereference: regitr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:553:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:553:24: note: Assignment 'regitr=(struct regitr_t*)calloc(1,sizeof(struct regitr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:555:29: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:556:5: warning: If memory allocation fails, then there is a possible null pointer dereference: itr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:554:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:554:20: note: Assignment 'regitr->itr=(struct _itr_t*)calloc(1,sizeof(struct _itr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:555:17: note: itr is assigned '(struct _itr_t*)regitr->itr' here.
pysam-0.23.0/bcftools/regidx.c:556:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:557:5: warning: If memory allocation fails, then there is a possible null pointer dereference: itr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:554:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:554:20: note: Assignment 'regitr->itr=(struct _itr_t*)calloc(1,sizeof(struct _itr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:555:17: note: itr is assigned '(struct _itr_t*)regitr->itr' here.
pysam-0.23.0/bcftools/regidx.c:557:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c:319:39: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
pysam-0.23.0/bcftools/regidx.c:315:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c:315:35: note: Assignment 'tmp_dat=malloc(regidx->payload_size*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c:319:39: note: Null pointer addition
pysam-0.23.0/bcftools/regidx.c:192:42: style:inconclusive: Function 'bcftools_regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:149:42: note: Function 'bcftools_regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
pysam-0.23.0/bcftools/regidx.c:192:42: note: Function 'bcftools_regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
pysam-0.23.0/bcftools/regidx.c:192:119: style:inconclusive: Function 'bcftools_regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:149:121: note: Function 'bcftools_regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c:192:119: note: Function 'bcftools_regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c:221:114: style:inconclusive: Function 'bcftools_regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:148:113: note: Function 'bcftools_regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c:221:114: note: Function 'bcftools_regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c:369:30: style:inconclusive: Function 'bcftools_regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:164:30: note: Function 'bcftools_regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c:369:30: note: Function 'bcftools_regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c:369:93: style:inconclusive: Function 'bcftools_regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:164:90: note: Function 'bcftools_regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:369:93: note: Function 'bcftools_regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:551:33: style:inconclusive: Function 'bcftools_regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:197:33: note: Function 'bcftools_regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c:551:33: note: Function 'bcftools_regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c:561:29: style:inconclusive: Function 'bcftools_regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:199:29: note: Function 'bcftools_regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c:561:29: note: Function 'bcftools_regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c:561:47: style:inconclusive: Function 'bcftools_regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:199:44: note: Function 'bcftools_regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:561:47: note: Function 'bcftools_regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:568:31: style:inconclusive: Function 'bcftools_regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:198:31: note: Function 'bcftools_regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:568:31: note: Function 'bcftools_regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:574:30: style:inconclusive: Function 'bcftools_regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:205:30: note: Function 'bcftools_regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:574:30: note: Function 'bcftools_regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:608:27: style:inconclusive: Function 'bcftools_regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:211:27: note: Function 'bcftools_regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:608:27: note: Function 'bcftools_regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c:100:35: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c:128:35: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c:128:45: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c:145:60: style: Parameter 'chr_end' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c:145:103: style: Parameter 'payload' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c:644:13: style: Variable 'src_itr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/regidx.c:44:14: style: struct member 'pos_t::pos' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/regidx.c:44:19: style: struct member 'pos_t::ireg' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/regidx.c.pysam.c:261:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/regidx.c.pysam.c:409:68: style: Condition 'list->reg[ireg].beg<=end' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/regidx.c.pysam.c:408:38: note: Assuming that condition 'list->reg[ireg].beg>end' is not redundant
pysam-0.23.0/bcftools/regidx.c.pysam.c:409:68: note: Condition 'list->reg[ireg].beg<=end' is always true
pysam-0.23.0/bcftools/regidx.c.pysam.c:595:63: style: Condition 'list->reg[i].beg<=itr->end' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/regidx.c.pysam.c:594:31: note: Assuming that condition 'list->reg[i].beg>itr->end' is not redundant
pysam-0.23.0/bcftools/regidx.c.pysam.c:595:63: note: Condition 'list->reg[i].beg<=itr->end' is always true
pysam-0.23.0/bcftools/regidx.c.pysam.c:247:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:247:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:248:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:248:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:249:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:249:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:250:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:250:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:251:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:246:21: note: Assignment 'idx=(struct regidx_t*)calloc(1,sizeof(struct regidx_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:251:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:314:42: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:314:42: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:315:19: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:315:19: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:320:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:320:31: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:331:31: warning: If memory allocation fails, then there is a possible null pointer dereference: ptr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:43: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:313:27: note: Assignment 'ptr=(struct reg_t**)malloc(sizeof(struct reg_t*)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:331:31: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:332:17: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_reg [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:328:45: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:328:30: note: Assignment 'tmp_reg=(struct reg_t*)malloc(sizeof(struct reg_t)*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:332:17: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:556:5: warning: If memory allocation fails, then there is a possible null pointer dereference: regitr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:555:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:555:24: note: Assignment 'regitr=(struct regitr_t*)calloc(1,sizeof(struct regitr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:556:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:557:29: warning: If memory allocation fails, then there is a possible null pointer dereference: regitr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:555:42: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:555:24: note: Assignment 'regitr=(struct regitr_t*)calloc(1,sizeof(struct regitr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:557:29: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:558:5: warning: If memory allocation fails, then there is a possible null pointer dereference: itr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:556:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:556:20: note: Assignment 'regitr->itr=(struct _itr_t*)calloc(1,sizeof(struct _itr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:557:17: note: itr is assigned '(struct _itr_t*)regitr->itr' here.
pysam-0.23.0/bcftools/regidx.c.pysam.c:558:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:559:5: warning: If memory allocation fails, then there is a possible null pointer dereference: itr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:556:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:556:20: note: Assignment 'regitr->itr=(struct _itr_t*)calloc(1,sizeof(struct _itr_t))', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:557:17: note: itr is assigned '(struct _itr_t*)regitr->itr' here.
pysam-0.23.0/bcftools/regidx.c.pysam.c:559:5: note: Null pointer dereference
pysam-0.23.0/bcftools/regidx.c.pysam.c:321:39: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
pysam-0.23.0/bcftools/regidx.c.pysam.c:317:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/regidx.c.pysam.c:317:35: note: Assignment 'tmp_dat=malloc(regidx->payload_size*list->nreg)', assigned value is 0
pysam-0.23.0/bcftools/regidx.c.pysam.c:321:39: note: Null pointer addition
pysam-0.23.0/bcftools/regidx.c.pysam.c:194:42: style:inconclusive: Function 'bcftools_regidx_init_string' argument 1 names different: declaration 'string' definition 'str'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:149:42: note: Function 'bcftools_regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:194:42: note: Function 'bcftools_regidx_init_string' argument 1 names different: declaration 'string' definition 'str'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:194:119: style:inconclusive: Function 'bcftools_regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:149:121: note: Function 'bcftools_regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:194:119: note: Function 'bcftools_regidx_init_string' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:223:114: style:inconclusive: Function 'bcftools_regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:148:113: note: Function 'bcftools_regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:223:114: note: Function 'bcftools_regidx_init' argument 5 names different: declaration 'usr' definition 'usr_dat'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:371:30: style:inconclusive: Function 'bcftools_regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:164:30: note: Function 'bcftools_regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:371:30: note: Function 'bcftools_regidx_overlap' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:371:93: style:inconclusive: Function 'bcftools_regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:164:90: note: Function 'bcftools_regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:371:93: note: Function 'bcftools_regidx_overlap' argument 5 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:553:33: style:inconclusive: Function 'bcftools_regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:197:33: note: Function 'bcftools_regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:553:33: note: Function 'bcftools_regitr_init' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:563:29: style:inconclusive: Function 'bcftools_regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:199:29: note: Function 'bcftools_regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:563:29: note: Function 'bcftools_regitr_reset' argument 1 names different: declaration 'idx' definition 'regidx'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:563:47: style:inconclusive: Function 'bcftools_regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:199:44: note: Function 'bcftools_regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:563:47: note: Function 'bcftools_regitr_reset' argument 2 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:570:31: style:inconclusive: Function 'bcftools_regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:198:31: note: Function 'bcftools_regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:570:31: note: Function 'bcftools_regitr_destroy' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:576:30: style:inconclusive: Function 'bcftools_regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:205:30: note: Function 'bcftools_regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:576:30: note: Function 'bcftools_regitr_overlap' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:610:27: style:inconclusive: Function 'bcftools_regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/regidx.h:211:27: note: Function 'bcftools_regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:610:27: note: Function 'bcftools_regitr_loop' argument 1 names different: declaration 'itr' definition 'regitr'.
pysam-0.23.0/bcftools/regidx.c.pysam.c:102:35: style: Parameter 'idx' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c.pysam.c:130:35: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c.pysam.c:130:45: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c.pysam.c:147:60: style: Parameter 'chr_end' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c.pysam.c:147:103: style: Parameter 'payload' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/regidx.c.pysam.c:646:13: style: Variable 'src_itr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/regidx.c.pysam.c:46:14: style: struct member 'pos_t::pos' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/regidx.c.pysam.c:46:19: style: struct member 'pos_t::ireg' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/khash_str2str.h:30:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/smpl_ilist.c:86:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/smpl_ilist.c:163:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/smpl_ilist.c:159:5: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c:156:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c:156:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c:159:5: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c:160:5: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c:156:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c:156:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c:160:5: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c:160:43: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c:156:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c:156:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c:160:43: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c:161:17: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c:156:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c:156:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c:161:17: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c:164:9: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c:156:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c:156:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c:164:9: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c:165:35: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c:156:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c:156:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c:165:35: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:88:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:165:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:161:5: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:161:5: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:162:5: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:162:5: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:162:43: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:162:43: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:163:17: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:163:17: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:166:9: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:166:9: note: Null pointer dereference
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:167:35: warning: If memory allocation fails, then there is a possible null pointer dereference: smpl [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:48: note: Assuming allocation function fails
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:158:26: note: Assignment 'smpl=(struct smpl_ilist_t*)calloc(1,sizeof(struct smpl_ilist_t))', assigned value is 0
pysam-0.23.0/bcftools/smpl_ilist.c.pysam.c:167:35: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c:49:6: warning: Possible null pointer dereference: tmp [nullPointer]
pysam-0.23.0/bcftools/str_finder.c:48:8: note: Assignment 'tmp=(*list)?(*list)->prev:NULL', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c:49:6: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c:113:13: warning:inconclusive: Possible null pointer dereference: tmp [nullPointer]
pysam-0.23.0/bcftools/str_finder.c:111:8: note: Assignment 'tmp=(*list)?(*list)->prev:NULL', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c:113:13: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c:114:10: warning:inconclusive: Possible null pointer dereference: tmp [nullPointer]
pysam-0.23.0/bcftools/str_finder.c:111:8: note: Assignment 'tmp=(*list)?(*list)->prev:NULL', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c:114:10: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c:333:11: warning: If memory allocation fails, then there is a possible null pointer dereference: str [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/str_finder.c:322:17: note: Assuming allocation function fails
pysam-0.23.0/bcftools/str_finder.c:322:17: note: Assignment 'str=calloc(1,len)', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c:333:11: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c:43:23: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/str_finder.c:73:3: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/str_finder.c:74:3: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/str_finder.c.pysam.c:51:6: warning: Possible null pointer dereference: tmp [nullPointer]
pysam-0.23.0/bcftools/str_finder.c.pysam.c:50:8: note: Assignment 'tmp=(*list)?(*list)->prev:NULL', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c.pysam.c:51:6: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c.pysam.c:115:13: warning:inconclusive: Possible null pointer dereference: tmp [nullPointer]
pysam-0.23.0/bcftools/str_finder.c.pysam.c:113:8: note: Assignment 'tmp=(*list)?(*list)->prev:NULL', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c.pysam.c:115:13: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c.pysam.c:116:10: warning:inconclusive: Possible null pointer dereference: tmp [nullPointer]
pysam-0.23.0/bcftools/str_finder.c.pysam.c:113:8: note: Assignment 'tmp=(*list)?(*list)->prev:NULL', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c.pysam.c:116:10: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c.pysam.c:335:11: warning: If memory allocation fails, then there is a possible null pointer dereference: str [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/str_finder.c.pysam.c:324:17: note: Assuming allocation function fails
pysam-0.23.0/bcftools/str_finder.c.pysam.c:324:17: note: Assignment 'str=calloc(1,len)', assigned value is 0
pysam-0.23.0/bcftools/str_finder.c.pysam.c:335:11: note: Null pointer dereference
pysam-0.23.0/bcftools/str_finder.c.pysam.c:45:23: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/str_finder.c.pysam.c:75:3: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/str_finder.c.pysam.c:76:3: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/tabix.c:37:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tbx_conf_gff [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/tabix.c:98:27: warning: If memory allocation fails, then there is a possible null pointer dereference: fn [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/tabix.c:97:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/tabix.c:97:18: note: Assignment 'fn=(char*)malloc(strlen(argv[optind])+5)', assigned value is 0
pysam-0.23.0/bcftools/tabix.c:98:27: note: Null pointer dereference
pysam-0.23.0/bcftools/tabix.c:99:29: warning: If memory allocation fails, then there is a possible null pointer dereference: fn [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/tabix.c:97:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/tabix.c:97:18: note: Assignment 'fn=(char*)malloc(strlen(argv[optind])+5)', assigned value is 0
pysam-0.23.0/bcftools/tabix.c:99:29: note: Null pointer dereference
pysam-0.23.0/bcftools/tabix.c:56:13: style: Statements following 'return' will never be executed. [unreachableCode]
pysam-0.23.0/bcftools/tabix.c.pysam.c:39:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tbx_conf_gff [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/tabix.c.pysam.c:100:27: warning: If memory allocation fails, then there is a possible null pointer dereference: fn [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/tabix.c.pysam.c:99:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/tabix.c.pysam.c:99:18: note: Assignment 'fn=(char*)malloc(strlen(argv[optind])+5)', assigned value is 0
pysam-0.23.0/bcftools/tabix.c.pysam.c:100:27: note: Null pointer dereference
pysam-0.23.0/bcftools/tabix.c.pysam.c:101:29: warning: If memory allocation fails, then there is a possible null pointer dereference: fn [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/tabix.c.pysam.c:99:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/tabix.c.pysam.c:99:18: note: Assignment 'fn=(char*)malloc(strlen(argv[optind])+5)', assigned value is 0
pysam-0.23.0/bcftools/tabix.c.pysam.c:101:29: note: Null pointer dereference
pysam-0.23.0/bcftools/tabix.c.pysam.c:58:13: style: Statements following 'return' will never be executed. [unreachableCode]
pysam-0.23.0/bcftools/tsv2vcf.c:35:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tsv [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/tsv2vcf.c:32:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/tsv2vcf.c:32:18: note: Assignment 'tsv=(struct tsv_t*)calloc(1,sizeof(struct tsv_t))', assigned value is 0
pysam-0.23.0/bcftools/tsv2vcf.c:35:5: note: Null pointer dereference
pysam-0.23.0/bcftools/tsv2vcf.c:105:27: style: Parameter 'tsv' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/tsv2vcf.c.pysam.c:37:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tsv [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/tsv2vcf.c.pysam.c:34:34: note: Assuming allocation function fails
pysam-0.23.0/bcftools/tsv2vcf.c.pysam.c:34:18: note: Assignment 'tsv=(struct tsv_t*)calloc(1,sizeof(struct tsv_t))', assigned value is 0
pysam-0.23.0/bcftools/tsv2vcf.c.pysam.c:37:5: note: Null pointer dereference
pysam-0.23.0/bcftools/tsv2vcf.c.pysam.c:107:27: style: Parameter 'tsv' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfannotate.c:283:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfannotate.c.pysam.c:285:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfbuf.c:127:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clean [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:268:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:286:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clean [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:365:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:395:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:439:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:501:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:560:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:657:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:706:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:737:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:867:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c:125:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c:124:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c:124:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c:125:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c:126:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c:124:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c:124:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c:126:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c:127:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c:124:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c:124:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c:127:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c:128:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c:124:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c:124:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c:128:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c:130:35: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c:124:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c:124:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c:130:35: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c:417:17: style: Local variable 'k1' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfbuf.c:405:13: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfbuf.c:417:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfbuf.c:418:17: style: Local variable 'k2' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfbuf.c:406:13: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfbuf.c:418:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfbuf.c:302:15: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:303:15: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:407:19: style: Variable 'rec1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:408:19: style: Variable 'rec2' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:463:15: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:464:15: style: Variable 'alt' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:512:36: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfbuf.c:512:47: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfbuf.c:521:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:522:16: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c:77:9: style: struct member 'overlap_t::rmme' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/vcfbuf.c:254:31: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:129:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clean [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:270:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:288:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clean [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:367:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:397:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:441:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:503:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:562:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:659:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:708:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:739:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:869:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:127:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:127:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:128:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:128:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:129:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:129:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:130:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:130:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:132:35: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:39: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:126:21: note: Assignment 'buf=(struct vcfbuf_t*)calloc(1,sizeof(struct vcfbuf_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:132:35: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:419:17: style: Local variable 'k1' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:407:13: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:419:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:420:17: style: Local variable 'k2' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:408:13: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:420:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:304:15: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:305:15: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:409:19: style: Variable 'rec1' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:410:19: style: Variable 'rec2' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:465:15: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:466:15: style: Variable 'alt' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:514:36: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:514:47: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:523:16: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:524:16: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:79:9: style: struct member 'overlap_t::rmme' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/vcfbuf.c.pysam.c:256:31: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
pysam-0.23.0/bcftools/vcfcall.c:293:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:360:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:372:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:431:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:488:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buffer [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:632:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_SR_REGIONS_OVERLAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:774:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:826:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:866:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:893:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:1023:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c:301:55: warning: If memory allocation fails, then there is a possible null pointer dereference: old2new [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfcall.c:300:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfcall.c:300:20: note: Assignment 'old2new=(int*)malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr))', assigned value is 0
pysam-0.23.0/bcftools/vcfcall.c:301:55: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfcall.c:1045:26: warning: Either the condition '!args.aux.prior_AC' is redundant or there is possible null pointer dereference: args.aux.prior_AC. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfcall.c:1044:22: note: Assuming that condition '!args.aux.prior_AC' is not redundant
pysam-0.23.0/bcftools/vcfcall.c:1045:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfcall.c:1148:16: style: Local variable 'is_indel' shadows outer function [shadowFunction]
pysam-0.23.0/bcftools/vcfcall.c:466:19: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfcall.c:1148:16: note: Shadow variable
pysam-0.23.0/bcftools/vcfcall.c:625:98: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c:625:187: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c:1127:32: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c:1127:65: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c:1127:98: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c:1129:32: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c:368:123: style: Parameter 'usr' can be declared as pointer to const. However it seems that 'tgt_parse' is a callback function, if 'usr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/vcfcall.c:625:52: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/vcfcall.c:368:123: note: Parameter 'usr' can be declared as pointer to const
pysam-0.23.0/bcftools/vcfcall.c:956:11: style: Variable 'ploidy_fname' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfcall.c:977:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:316:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:362:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:433:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:490:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buffer [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:634:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_SR_REGIONS_OVERLAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:776:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1025:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:303:55: warning: If memory allocation fails, then there is a possible null pointer dereference: old2new [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:302:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:302:20: note: Assignment 'old2new=(int*)malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr))', assigned value is 0
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:303:55: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1047:26: warning: Either the condition '!args.aux.prior_AC' is redundant or there is possible null pointer dereference: args.aux.prior_AC. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1046:22: note: Assuming that condition '!args.aux.prior_AC' is not redundant
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1047:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1150:16: style: Local variable 'is_indel' shadows outer function [shadowFunction]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:468:19: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1150:16: note: Shadow variable
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:627:98: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:627:187: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1129:32: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1129:65: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1129:98: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:1131:32: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:370:123: style: Parameter 'usr' can be declared as pointer to const. However it seems that 'tgt_parse' is a callback function, if 'usr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:627:52: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:370:123: note: Parameter 'usr' can be declared as pointer to const
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:958:11: style: Variable 'ploidy_fname' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfcall.c.pysam.c:979:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfcnv.c:109:7: error: There is an unknown macro here somewhere. Configuration is required. If open_file is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfcnv.c.pysam.c:111:7: error: There is an unknown macro here somewhere. Configuration is required. If open_file is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfconcat.c:94:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:271:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:283:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:419:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:505:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:764:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:788:109: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:811:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:855:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:959:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:1038:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c:999:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:999:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:999:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:999:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:1000:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:1000:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:1001:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:1001:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:1002:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:1002:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:1003:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:1003:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:1004:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:1004:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:1005:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:1005:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:1006:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c:998:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c:998:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c:1006:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c:202:19: style: Local variable 'str' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconcat.c:95:15: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconcat.c:202:19: note: Shadow variable
pysam-0.23.0/bcftools/vcfconcat.c:71:46: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfconcat.c:1008:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:126:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:273:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:285:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:421:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:507:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:766:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:790:109: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_CTG [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:837:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bgzf [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:857:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1040:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1001:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1001:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1001:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1001:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1002:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1002:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1003:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1003:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1004:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1004:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1005:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1005:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1006:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1006:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1007:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1007:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1008:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1000:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1008:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:204:19: style: Local variable 'str' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:97:15: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:204:19: note: Shadow variable
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:73:46: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfconcat.c.pysam.c:1010:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfconvert.c:99:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_SR_REGIONS_OVERLAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:295:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:347:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:433:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:599:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:734:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:853:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:922:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1046:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1194:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1295:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1325:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1400:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1479:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1522:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1605:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:1730:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c:210:13: style: Redundant condition: The condition '*se' is redundant since '*se == '_'' is sufficient. [redundantCondition]
pysam-0.23.0/bcftools/vcfconvert.c:926:9: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/vcfconvert.c:923:9: note: First condition
pysam-0.23.0/bcftools/vcfconvert.c:926:9: note: Second condition
pysam-0.23.0/bcftools/vcfconvert.c:1051:9: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/vcfconvert.c:1048:9: note: First condition
pysam-0.23.0/bcftools/vcfconvert.c:1051:9: note: Second condition
pysam-0.23.0/bcftools/vcfconvert.c:1198:9: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/vcfconvert.c:1195:9: note: First condition
pysam-0.23.0/bcftools/vcfconvert.c:1198:9: note: Second condition
pysam-0.23.0/bcftools/vcfconvert.c:1229:18: style: Condition 'hap_fname' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/vcfconvert.c:139:17: warning: If memory allocation fails, then there is a possible null pointer dereference: samples [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:136:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:136:23: note: Assignment 'samples=(int*)malloc(sizeof(int)*nsamples)', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:139:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:587:10: warning: Either the condition '!se' is redundant or there is possible null pointer dereference: se. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:585:14: note: Assuming that condition '!se' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:587:10: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1328:5: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:1325:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:1328:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1328:22: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:1325:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:1328:22: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1329:26: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:1325:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:1329:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1585:39: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:1584:18: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:1585:39: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1680:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1680:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1680:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1680:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1681:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1681:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1682:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1682:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1683:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1683:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1684:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1684:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1685:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1685:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1686:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1686:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:1687:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c:1679:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c:1679:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c:1687:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c:454:22: warning: Either the condition '!sc' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:452:18: note: Assuming that condition '!sc' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:454:22: note: Null pointer subtraction
pysam-0.23.0/bcftools/vcfconvert.c:590:33: warning: Either the condition '!se' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:585:14: note: Assuming that condition '!se' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:590:33: note: Null pointer addition
pysam-0.23.0/bcftools/vcfconvert.c:606:22: warning: Either the condition '!se' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:605:10: note: Assuming that condition '!se' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:606:22: note: Null pointer subtraction
pysam-0.23.0/bcftools/vcfconvert.c:754:18: warning: Either the condition '!sc' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c:752:10: note: Assuming that condition '!sc' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c:754:18: note: Null pointer subtraction
pysam-0.23.0/bcftools/vcfconvert.c:931:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c:896:22: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c:931:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c:989:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c:892:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c:989:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c:1056:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c:1015:22: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c:1056:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c:1203:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c:1168:22: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c:1203:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c:243:13: style: Variable 'args' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c:251:13: style: Variable 'args' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c:259:54: style: Parameter 'rec' can be declared as pointer to const. However it seems that 'tsv_setter_verify_pos' is a callback function, if 'rec' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/vcfconvert.c:775:30: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/vcfconvert.c:259:54: note: Parameter 'rec' can be declared as pointer to const
pysam-0.23.0/bcftools/vcfconvert.c:326:35: style: Parameter 'tsv' can be declared as pointer to const. However it seems that 'tsv_setter_haps' is a callback function, if 'tsv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/vcfconvert.c:777:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/vcfconvert.c:326:35: note: Parameter 'tsv' can be declared as pointer to const
pysam-0.23.0/bcftools/vcfconvert.c:339:15: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c:445:15: style: Variable 'sc' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c:1288:64: style: Parameter 'se' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfconvert.c:1689:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:101:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_SR_REGIONS_OVERLAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:365:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:435:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:601:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:736:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:855:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:938:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1063:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1210:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1297:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1327:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1402:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1481:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1524:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1732:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:212:13: style: Redundant condition: The condition '*se' is redundant since '*se == '_'' is sufficient. [redundantCondition]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:928:9: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:925:9: note: First condition
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:928:9: note: Second condition
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1053:9: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1050:9: note: First condition
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1053:9: note: Second condition
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1200:9: style: The if condition is the same as the previous if condition [duplicateCondition]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1197:9: note: First condition
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1200:9: note: Second condition
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1231:18: style: Condition 'hap_fname' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:141:17: warning: If memory allocation fails, then there is a possible null pointer dereference: samples [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:138:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:138:23: note: Assignment 'samples=(int*)malloc(sizeof(int)*nsamples)', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:141:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:589:10: warning: Either the condition '!se' is redundant or there is possible null pointer dereference: se. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:587:14: note: Assuming that condition '!se' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:589:10: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1330:5: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1327:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1330:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1330:22: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1327:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1330:22: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1331:26: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1327:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1331:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1587:39: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1586:18: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1587:39: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1682:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1682:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1682:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1682:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1683:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1683:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1684:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1684:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1685:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1685:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1686:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1686:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1687:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1687:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1688:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1688:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1689:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1681:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1689:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:456:22: warning: Either the condition '!sc' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:454:18: note: Assuming that condition '!sc' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:456:22: note: Null pointer subtraction
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:592:33: warning: Either the condition '!se' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:587:14: note: Assuming that condition '!se' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:592:33: note: Null pointer addition
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:608:22: warning: Either the condition '!se' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:607:10: note: Assuming that condition '!se' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:608:22: note: Null pointer subtraction
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:756:18: warning: Either the condition '!sc' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:754:10: note: Assuming that condition '!sc' is not redundant
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:756:18: note: Null pointer subtraction
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:933:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:898:22: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:933:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:991:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:894:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:991:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1058:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1017:22: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1058:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1205:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1170:22: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1205:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:245:13: style: Variable 'args' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:253:13: style: Variable 'args' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:261:54: style: Parameter 'rec' can be declared as pointer to const. However it seems that 'tsv_setter_verify_pos' is a callback function, if 'rec' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:777:30: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:261:54: note: Parameter 'rec' can be declared as pointer to const
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:328:35: style: Parameter 'tsv' can be declared as pointer to const. However it seems that 'tsv_setter_haps' is a callback function, if 'tsv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:779:31: note: You might need to cast the function pointer here
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:328:35: note: Parameter 'tsv' can be declared as pointer to const
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:341:15: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:447:15: style: Variable 'sc' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1290:64: style: Parameter 'se' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfconvert.c.pysam.c:1691:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcffilter.c:90:99: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c:230:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c:268:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c:405:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c:446:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c:471:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c:546:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c:101:22: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:100:32: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:100:32: note: Assignment 'rmme=strdup(args->mask_negate?args->mask_list+1:args->mask_list)', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:100:94: note: Assignment 'tmp=rmme', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:101:22: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:505:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:505:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:505:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:505:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:506:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:506:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:507:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:507:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:508:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:508:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:509:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:509:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:510:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:510:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:511:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:511:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:515:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c:504:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c:504:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c:515:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c:664:19: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcffilter.c:542:11: note: Shadowed declaration
pysam-0.23.0/bcftools/vcffilter.c:664:19: note: Shadow variable
pysam-0.23.0/bcftools/vcffilter.c:455:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcffilter.c:456:19: style: Variable 'alt' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:92:99: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:232:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:270:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:407:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_gt_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:448:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:548:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:103:22: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:102:32: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:102:32: note: Assignment 'rmme=strdup(args->mask_negate?args->mask_list+1:args->mask_list)', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:102:94: note: Assignment 'tmp=rmme', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:103:22: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:507:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:507:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:507:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:507:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:508:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:508:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:509:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:509:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:510:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:510:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:511:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:511:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:512:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:512:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:513:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:513:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:517:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:506:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:517:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:666:19: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:544:11: note: Shadowed declaration
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:666:19: note: Shadow variable
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:457:19: style: Variable 'ref' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcffilter.c.pysam.c:458:19: style: Variable 'alt' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:174:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:238:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:258:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_SR_REGIONS_OVERLAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:479:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:485:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:543:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:621:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:1110:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:1142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:1223:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c:101:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:101:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:104:28: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:104:28: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:106:9: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:104:19: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfgtcheck.c:106:9: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:106:37: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:104:19: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfgtcheck.c:106:37: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:203:12: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:202:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:202:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:203:12: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:204:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:202:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:202:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:204:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:205:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:202:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:202:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:205:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:206:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:202:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:202:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:206:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:207:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:202:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:202:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:207:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:208:12: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:202:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:202:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:208:12: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:990:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:977:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:977:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:990:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:991:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:977:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:977:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:991:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:994:19: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:977:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:977:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:994:19: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:999:27: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:977:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:977:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:999:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1000:57: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:977:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:977:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1000:57: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1000:71: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:977:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:977:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1000:71: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1042:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1029:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1029:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*narr)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1042:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1043:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1029:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1029:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*narr)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1043:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1197:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1197:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1198:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1198:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1199:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1199:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1200:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1200:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1201:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1201:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1202:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1202:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1203:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1203:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1209:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1209:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1211:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1211:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1217:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1217:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1218:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1218:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:1333:43: warning: Either the condition '!list' is redundant or there is possible null pointer dereference: list. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfgtcheck.c:1332:26: note: Assuming that condition '!list' is not redundant
pysam-0.23.0/bcftools/vcfgtcheck.c:1333:43: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c:999:21: style: Local variable 'idx' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfgtcheck.c:981:17: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfgtcheck.c:999:21: note: Shadow variable
pysam-0.23.0/bcftools/vcfgtcheck.c:1066:21: style: Local variable 'idx' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfgtcheck.c:1030:19: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfgtcheck.c:1066:21: note: Shadow variable
pysam-0.23.0/bcftools/vcfgtcheck.c:643:33: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfgtcheck.c:133:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:134:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:160:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:161:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:213:19: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:823:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:824:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c:1220:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfgtcheck.c:175:16: style: Variable 'nsites' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:183:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KBS_ELTBITS [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:240:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:260:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_SR_REGIONS_OVERLAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:481:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:487:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:545:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:623:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1112:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1225:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:103:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:103:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:106:28: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:106:28: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:108:9: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:106:19: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:108:9: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:108:37: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:53: note: Calling function 'set_cwd', 1st argument 'args' value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:106:19: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:108:37: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:205:12: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:205:12: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:206:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:206:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:207:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:207:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:208:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:208:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:209:5: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:209:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:210:12: warning: If memory allocation fails, then there is a possible null pointer dereference: dat [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:47: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:204:25: note: Assignment 'dat=(struct diff_sites_t*)malloc(args->diff_sites_size)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:210:12: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:992:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:992:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:993:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:993:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:996:19: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:996:19: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1001:27: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1001:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1002:57: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1002:57: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1002:71: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:979:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*args->ngt_smpl)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1002:71: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1044:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1031:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1031:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*narr)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1044:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1045:17: warning: If memory allocation fails, then there is a possible null pointer dereference: arr [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1031:38: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1031:23: note: Assignment 'arr=(struct idbl_t*)malloc(sizeof(*arr)*narr)', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1045:17: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1199:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1199:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1200:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1200:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1201:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1201:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1202:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1202:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1203:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1203:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1204:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1204:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1205:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1205:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1211:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1211:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1213:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1213:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1219:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1219:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1220:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1220:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1335:43: warning: Either the condition '!list' is redundant or there is possible null pointer dereference: list. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1334:26: note: Assuming that condition '!list' is not redundant
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1335:43: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1001:21: style: Local variable 'idx' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:983:17: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1001:21: note: Shadow variable
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1068:21: style: Local variable 'idx' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1032:19: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1068:21: note: Shadow variable
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:645:33: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:135:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:136:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:162:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:163:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:215:19: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:825:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:826:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1222:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:177:16: style: Variable 'nsites' is assigned a value that is never used. [unreadVariable]
pysam-0.23.0/bcftools/vcfhead.c:69:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfhead.c.pysam.c:77:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfindex.c:49:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfindex.c:89:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_IDX_DELIM [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfindex.c:253:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfindex.c:101:9: warning: If memory allocation fails, then there is a possible null pointer dereference: fname [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfindex.c:99:24: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfindex.c:99:24: note: Assignment 'fntemp=strdup(fname)', assigned value is 0
pysam-0.23.0/bcftools/vcfindex.c:100:16: note: fname is assigned 'fntemp' here.
pysam-0.23.0/bcftools/vcfindex.c:101:9: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfindex.c:130:17: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfindex.c:87:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfindex.c:130:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfindex.c:186:13: style: Local variable 'ret' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfindex.c:72:24: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfindex.c:186:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfindex.c:153:15: style: Variable 'ext' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfindex.c:164:15: style: Variable 'ext' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfindex.c:229:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:91:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_IDX_DELIM [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:255:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:103:9: warning: If memory allocation fails, then there is a possible null pointer dereference: fname [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:101:24: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:101:24: note: Assignment 'fntemp=strdup(fname)', assigned value is 0
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:102:16: note: fname is assigned 'fntemp' here.
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:103:9: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:132:17: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:89:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:132:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:188:13: style: Local variable 'ret' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:74:24: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:188:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:155:15: style: Variable 'ext' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:166:15: style: Variable 'ext' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfindex.c.pysam.c:231:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfisec.c:110:8: error: There is an unknown macro here somewhere. Configuration is required. If HTS_FORMAT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfisec.c.pysam.c:112:8: error: There is an unknown macro here somewhere. Configuration is required. If HTS_FORMAT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfmerge.c:51:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfmerge.c.pysam.c:53:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfnorm.c:164:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:327:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:342:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:395:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:469:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:525:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:781:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:820:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:886:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:905:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1079:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1099:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1229:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1401:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1410:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1417:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1487:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1522:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1716:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1725:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1851:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1944:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_ANY [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1963:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:1984:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_ANY [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2043:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2095:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable str2int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2131:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2167:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2243:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2288:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2347:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_ANY [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2372:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2436:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:2496:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_BOTH [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c:347:14: style: Condition 'inf' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/vcfnorm.c:159:19: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: seq. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfnorm.c:530:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfnorm.c:531:18: note: Calling function 'seq_to_upper', 1st argument 'ref' value is 0
pysam-0.23.0/bcftools/vcfnorm.c:159:19: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:180:41: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfnorm.c:174:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfnorm.c:180:41: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2488:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2488:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2488:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2488:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2489:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2489:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2490:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2490:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2491:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2491:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2492:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2492:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2493:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2493:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2494:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2494:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2495:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2495:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2496:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2496:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2497:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2497:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2498:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2498:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2499:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2499:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2502:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2502:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2503:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2503:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:2506:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c:2487:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c:2487:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c:2506:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c:784:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c:1082:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c:1404:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c:1719:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c:300:15: style: Same expression used in consecutive assignments of 'nals' and 'nals_ori'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/vcfnorm.c:300:38: note: Same expression used in consecutive assignments of 'nals' and 'nals_ori'.
pysam-0.23.0/bcftools/vcfnorm.c:300:15: note: Same expression used in consecutive assignments of 'nals' and 'nals_ori'.
pysam-0.23.0/bcftools/vcfnorm.c:193:9: style: Local variable 'has_non_acgtn' shadows outer function [shadowFunction]
pysam-0.23.0/bcftools/vcfnorm.c:141:19: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c:193:9: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c:169:13: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfnorm.c:166:31: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c:169:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c:216:17: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfnorm.c:166:31: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c:216:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c:233:13: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfnorm.c:166:31: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c:233:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c:143:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c:346:21: style: Variable 'inf' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c:378:23: style: Variable 'tr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c:793:65: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c:1161:19: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c:1161:30: style: Variable 'sx' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c:1485:18: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c:1769:57: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c:1959:36: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c:1959:50: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c:2075:49: style: Parameter 'ca' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c:2508:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:166:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:329:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:344:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:397:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:471:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:527:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:783:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:822:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:888:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:907:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1081:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1101:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1231:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1403:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1412:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1419:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1489:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1524:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1718:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1727:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1853:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1946:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_ANY [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1965:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rid [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1986:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_ANY [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2045:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2097:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable str2int [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2133:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2169:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2245:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2290:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2349:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_ANY [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2374:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2498:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COLLAPSE_BOTH [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:349:14: style: Condition 'inf' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:161:19: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: seq. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:532:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:533:18: note: Calling function 'seq_to_upper', 1st argument 'ref' value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:161:19: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:182:41: warning: Either the condition '!ref' is redundant or there is possible null pointer dereference: ref. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:176:10: note: Assuming that condition '!ref' is not redundant
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:182:41: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2490:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2490:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2490:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2490:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2491:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2491:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2492:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2492:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2493:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2493:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2494:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2494:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2495:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2495:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2496:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2496:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2497:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2497:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2498:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2498:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2499:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2499:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2500:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2500:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2501:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2501:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2504:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2504:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2505:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2505:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2508:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2489:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2508:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:786:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1084:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1406:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1721:27: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:302:15: style: Same expression used in consecutive assignments of 'nals' and 'nals_ori'. [duplicateAssignExpression]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:302:38: note: Same expression used in consecutive assignments of 'nals' and 'nals_ori'.
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:302:15: note: Same expression used in consecutive assignments of 'nals' and 'nals_ori'.
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:195:9: style: Local variable 'has_non_acgtn' shadows outer function [shadowFunction]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:143:19: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:195:9: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:171:13: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:168:31: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:171:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:218:17: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:168:31: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:218:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:235:13: style: Local variable 'len' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:168:31: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:235:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:145:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:348:21: style: Variable 'inf' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:380:23: style: Variable 'tr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:795:65: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1163:19: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1163:30: style: Variable 'sx' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1487:18: style: Variable 'src' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1771:57: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1961:36: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:1961:50: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2077:49: style: Parameter 'ca' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfnorm.c.pysam.c:2510:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfplugin.c:840:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c:74:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c:130:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c:191:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c:233:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c:304:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c:94:13: warning: If memory allocation fails, then there is a possible null pointer dereference: samples [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c:92:32: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c:92:19: note: Assignment 'samples=(int*)malloc(sizeof(int)*nsamples)', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c:94:13: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c:218:28: warning: If memory allocation fails, then there is a possible null pointer dereference: dst [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c:216:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c:216:18: note: Assignment 'dst=(char**)malloc(sizeof(char*)*nsrc)', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c:218:28: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c:269:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c:268:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c:268:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c:269:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c:269:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c:268:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c:268:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c:269:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c:270:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c:268:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c:268:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c:270:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c:186:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfquery.c:179:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfquery.c:186:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfquery.c:221:38: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfquery.c:275:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:76:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:132:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:193:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:306:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:96:13: warning: If memory allocation fails, then there is a possible null pointer dereference: samples [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:94:32: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:94:19: note: Assignment 'samples=(int*)malloc(sizeof(int)*nsamples)', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:96:13: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:220:28: warning: If memory allocation fails, then there is a possible null pointer dereference: dst [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:218:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:218:18: note: Assignment 'dst=(char**)malloc(sizeof(char*)*nsrc)', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:220:28: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:271:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:270:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:270:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:271:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:271:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:270:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:270:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:271:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:272:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:270:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:270:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:272:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:188:13: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:181:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:188:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:223:38: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfquery.c.pysam.c:277:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfroh.c:144:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:392:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:533:148: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:693:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:778:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:822:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:828:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:1058:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:1074:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:1166:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c:1121:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c:1120:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c:1120:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c:1121:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c:1121:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c:1120:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c:1120:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c:1121:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c:1122:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c:1120:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c:1120:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c:1122:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c:1123:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c:1120:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c:1120:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c:1123:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c:1124:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c:1120:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c:1120:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c:1124:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c:1125:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c:1120:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c:1120:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c:1125:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c:1183:41: style: Same expression on both sides of '||'. [duplicateExpression]
pysam-0.23.0/bcftools/vcfroh.c:466:13: style: Variable 'args' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:520:17: style: Variable 'fwd' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:523:18: style: Variable 'vpath' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:646:18: style: Variable 'vpath' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:653:21: style: Variable 'pval' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:661:44: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfroh.c:672:17: style: Variable 'str' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:689:24: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfroh.c:722:17: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:775:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:776:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:777:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:818:27: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfroh.c:947:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:948:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:949:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c:1130:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:146:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:394:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_SEP_LINE [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:535:148: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:695:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:824:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:830:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1168:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1123:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1123:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1123:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1123:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1124:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1124:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1125:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1125:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1126:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1126:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1127:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1122:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1127:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1185:41: style: Same expression on both sides of '||'. [duplicateExpression]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:468:13: style: Variable 'args' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:522:17: style: Variable 'fwd' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:525:18: style: Variable 'vpath' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:648:18: style: Variable 'vpath' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:655:21: style: Variable 'pval' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:663:44: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:674:17: style: Variable 'str' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:691:24: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:724:17: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:777:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:778:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:779:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:820:27: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:949:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:950:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:951:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfroh.c.pysam.c:1132:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfsom.c:87:7: error: There is an unknown macro here somewhere. Configuration is required. If open_file is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfsom.c.pysam.c:89:7: error: There is an unknown macro here somewhere. Configuration is required. If open_file is a macro then please configure it. [unknownMacro]
pysam-0.23.0/bcftools/vcfsort.c:93:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:184:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:229:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:263:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:380:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:420:124: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:458:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:510:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:561:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:578:105: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:682:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:696:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:750:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:790:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c:684:5: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfsort.c:211:21: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:459:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c:211:21: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:212:22: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:459:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c:212:22: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:213:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:459:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c:213:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:214:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:459:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c:214:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:215:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:459:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c:215:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:229:9: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:456:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:459:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c:229:9: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:751:25: warning: Either the condition '!tmp' is redundant or there is possible null pointer dereference: tmp. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfsort.c:750:14: note: Assuming that condition '!tmp' is not redundant
pysam-0.23.0/bcftools/vcfsort.c:751:25: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:769:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:768:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:768:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:769:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:769:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:768:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:768:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:769:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:770:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:768:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:768:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:770:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:771:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:768:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:768:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:771:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:772:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c:768:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c:768:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c:772:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c:120:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:121:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:130:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:131:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:154:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:155:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:181:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:182:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:212:14: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:749:15: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c:774:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfsort.c:444:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfsort.c:445:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfsort.c:446:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfsort.c:447:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:186:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:231:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:265:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:382:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:422:124: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:460:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:512:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIhts_pos [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:563:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:580:105: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:684:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:752:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:792:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:686:5: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:213:21: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:461:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:213:21: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:214:22: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:461:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:214:22: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:215:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:461:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:215:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:216:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:461:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:216:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:217:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:461:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:217:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:231:9: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: dest [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:458:35: note: Assignment 'tmp=malloc(sizeof(*tmp)+rec->unpack_size[1]*sizeof(bcf1_t*))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:461:23: note: Calling function 'pack_bcf_data', 1st argument 'tmp' value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:231:9: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:753:25: warning: Either the condition '!tmp' is redundant or there is possible null pointer dereference: tmp. [nullPointerRedundantCheck]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:752:14: note: Assuming that condition '!tmp' is not redundant
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:753:25: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:771:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:771:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:771:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:771:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:772:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:772:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:773:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:773:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:774:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:770:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:774:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:122:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:123:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:132:13: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:133:13: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:156:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:157:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:183:19: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:184:19: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:214:14: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:751:15: style: Variable 'tmp' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:776:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:446:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:447:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:448:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:449:11: warning: Suspicious usage of 'sizeof' with a numeric constant as parameter. [sizeofwithnumericparameter]
pysam-0.23.0/bcftools/vcfstats.c:419:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:444:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:666:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:728:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_INDEL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:822:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_REAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:858:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_SNP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:906:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:923:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:932:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:945:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_SNP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:960:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:994:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNKN [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:1116:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNKN [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:1279:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_REF [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:1316:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fname [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:1367:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:1876:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:1951:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c:1273:38: error: Array 'args->stats[3]' accessed at index -1, which is out of bounds. [negativeIndex]
pysam-0.23.0/bcftools/vcfstats.c:1250:19: note: Assignment 'ret=0', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1251:20: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfstats.c:1273:38: note: Negative array index
pysam-0.23.0/bcftools/vcfstats.c:1516:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c:1516:17: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c:1516:17: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c:1516:17: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c:1828:17: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c:274:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ctx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:273:46: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:273:24: note: Assignment 'ctx=(struct indel_ctx_t*)calloc(1,sizeof(struct indel_ctx_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:274:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:275:11: warning: If memory allocation fails, then there is a possible null pointer dereference: ctx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:273:46: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:273:24: note: Assignment 'ctx=(struct indel_ctx_t*)calloc(1,sizeof(struct indel_ctx_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:275:11: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:639:20: warning: Possible null pointer dereference: reader [nullPointer]
pysam-0.23.0/bcftools/vcfstats.c:1248:28: note: Assignment 'reader=NULL', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1251:20: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfstats.c:1271:24: note: Calling function 'init_iaf', 2nd argument 'reader' value is 0
pysam-0.23.0/bcftools/vcfstats.c:639:20: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:1915:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:1914:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:1914:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1915:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:1916:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:1914:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:1914:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1916:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:1916:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:1914:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:1914:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1916:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:1917:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:1914:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:1914:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1917:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:1917:23: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:1914:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:1914:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1917:23: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:1917:43: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c:1914:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c:1914:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1917:43: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c:923:88: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c:924:90: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c:925:90: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c:960:92: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c:961:94: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c:962:94: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c:1170:13: style: Local variable 'is' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfstats.c:1103:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c:1170:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c:1227:31: style: Local variable 'reader' shadows outer argument [shadowArgument]
pysam-0.23.0/bcftools/vcfstats.c:1088:69: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c:1227:31: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c:1527:17: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfstats.c:1349:12: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c:1527:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c:1821:21: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfstats.c:1349:12: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c:1821:21: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c:1236:35: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1414:70: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1426:27: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1648:26: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1649:66: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1650:66: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1651:66: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1683:95: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:1807:119: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c:221:43: style: Parameter 'ctx' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:221:54: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:301:75: style: Parameter 'alt' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:407:37: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:892:34: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:892:51: style: Parameter 'ad_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:906:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:907:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:908:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:914:52: style: Parameter 'ad_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:950:73: style: Parameter 'ad_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:950:96: style: Parameter 'dp_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c:981:32: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:982:32: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:983:32: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1227:31: style: Variable 'reader' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1370:18: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1470:18: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1526:27: style: Variable 'usr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1540:18: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1700:22: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1821:25: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1861:22: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c:1922:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfstats.c:104:11: style: struct member 'stats_t::vaf' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:421:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:446:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:668:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:730:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_INDEL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:824:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HT_REAL [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:860:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_SNP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:908:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:925:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_vector_end [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:934:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:947:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_SNP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:962:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int8_missing [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:996:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNKN [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1118:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GT_UNKN [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1281:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_REF [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1318:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fname [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1369:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1953:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1275:38: error: Array 'args->stats[3]' accessed at index -1, which is out of bounds. [negativeIndex]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1252:19: note: Assignment 'ret=0', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1253:20: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1275:38: note: Negative array index
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:928:112: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1518:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1518:17: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1518:17: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1518:17: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1830:17: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:276:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ctx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:275:46: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:275:24: note: Assignment 'ctx=(struct indel_ctx_t*)calloc(1,sizeof(struct indel_ctx_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:276:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:277:11: warning: If memory allocation fails, then there is a possible null pointer dereference: ctx [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:275:46: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:275:24: note: Assignment 'ctx=(struct indel_ctx_t*)calloc(1,sizeof(struct indel_ctx_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:277:11: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:641:20: warning: Possible null pointer dereference: reader [nullPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1250:28: note: Assignment 'reader=NULL', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1253:20: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1273:24: note: Calling function 'init_iaf', 2nd argument 'reader' value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:641:20: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1917:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1917:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1918:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1918:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1918:26: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1918:26: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1919:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1919:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1919:23: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1919:23: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1919:43: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1916:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1919:43: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:925:88: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:926:90: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:927:90: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:962:92: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:963:94: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:964:94: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1172:13: style: Local variable 'is' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1105:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1172:13: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1229:31: style: Local variable 'reader' shadows outer argument [shadowArgument]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1090:69: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1229:31: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1529:17: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1351:12: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1529:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1823:21: style: Local variable 'j' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1351:12: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1823:21: note: Shadow variable
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1238:35: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1416:88: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1428:27: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1650:26: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1651:66: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1652:66: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1653:66: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1685:113: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1809:137: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:223:43: style: Parameter 'ctx' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:223:54: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:303:75: style: Parameter 'alt' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:409:37: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:894:34: style: Parameter 'line' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:894:51: style: Parameter 'ad_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:908:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:909:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:910:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:916:52: style: Parameter 'ad_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:952:73: style: Parameter 'ad_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:952:96: style: Parameter 'dp_fmt_ptr' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:983:32: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:984:32: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:985:32: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1229:31: style: Variable 'reader' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1372:18: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1472:18: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1528:27: style: Variable 'usr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1542:18: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1702:22: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1823:25: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1863:22: style: Variable 'stats' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1924:26: style: Variable 'loptions' can be declared as const array [constVariable]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:106:11: style: struct member 'stats_t::vaf' is never used. [unusedStructMember]
pysam-0.23.0/bcftools/vcfview.c:90:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c:277:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c:342:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c:508:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c:630:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c:464:18: style: Condition 'args->trim_star_allele' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/vcfview.c:181:21: error: Common realloc mistake: 'type_list' nulled but not freed upon failure [memleakOnRealloc]
pysam-0.23.0/bcftools/vcfview.c:189:9: error: Common realloc mistake: 'type_list' nulled but not freed upon failure [memleakOnRealloc]
pysam-0.23.0/bcftools/vcfview.c:562:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:562:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:562:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:562:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:563:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:563:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:564:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:564:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:565:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:565:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:566:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:566:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:567:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:567:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:568:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:568:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:569:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:569:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:570:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:570:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:571:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:571:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:571:20: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:571:20: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:571:35: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:571:35: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:571:50: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:571:50: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:572:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:572:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:573:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c:561:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c:561:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c:573:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c:246:17: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfview.c:89:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfview.c:246:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfview.c:787:19: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfview.c:623:11: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfview.c:787:19: note: Shadow variable
pysam-0.23.0/bcftools/vcfview.c:278:16: style: Variable 'fmt_ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfview.c:506:27: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:92:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable header [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:279:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:344:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:632:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:466:18: style: Condition 'args->trim_star_allele' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:183:21: error: Common realloc mistake: 'type_list' nulled but not freed upon failure [memleakOnRealloc]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:191:9: error: Common realloc mistake: 'type_list' nulled but not freed upon failure [memleakOnRealloc]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:564:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:564:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:564:27: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:564:27: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:565:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:565:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:566:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:566:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:567:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:567:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:568:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:568:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:569:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:569:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:570:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:570:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:571:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:571:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:572:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:572:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:20: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:20: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:35: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:35: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:50: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:573:50: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:574:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:574:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:575:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [nullPointerOutOfMemory]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:37: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfview.c.pysam.c:563:21: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfview.c.pysam.c:575:5: note: Null pointer dereference
pysam-0.23.0/bcftools/vcfview.c.pysam.c:248:17: style: Local variable 'i' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:91:9: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfview.c.pysam.c:248:17: note: Shadow variable
pysam-0.23.0/bcftools/vcfview.c.pysam.c:789:19: style: Local variable 'tmp' shadows outer variable [shadowVariable]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:625:11: note: Shadowed declaration
pysam-0.23.0/bcftools/vcfview.c.pysam.c:789:19: note: Shadow variable
pysam-0.23.0/bcftools/vcfview.c.pysam.c:280:16: style: Variable 'fmt_ptr' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcfview.c.pysam.c:508:27: style: Parameter 'args' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcmp.c:122:42: style:inconclusive: Function 'vcmp_map_ARvalues' argument 2 names different: declaration 'number' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/vcmp.h:59:42: note: Function 'vcmp_map_ARvalues' argument 2 names different: declaration 'number' definition 'n'.
pysam-0.23.0/bcftools/vcmp.c:122:42: note: Function 'vcmp_map_ARvalues' argument 2 names different: declaration 'number' definition 'n'.
pysam-0.23.0/bcftools/vcmp.c:59:11: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcmp.c:59:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcmp.c:87:30: style: Parameter 'vcmp' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcmp.c:92:15: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcmp.c:92:29: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcmp.c.pysam.c:124:42: style:inconclusive: Function 'vcmp_map_ARvalues' argument 2 names different: declaration 'number' definition 'n'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/vcmp.h:59:42: note: Function 'vcmp_map_ARvalues' argument 2 names different: declaration 'number' definition 'n'.
pysam-0.23.0/bcftools/vcmp.c.pysam.c:124:42: note: Function 'vcmp_map_ARvalues' argument 2 names different: declaration 'number' definition 'n'.
pysam-0.23.0/bcftools/vcmp.c.pysam.c:61:11: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcmp.c.pysam.c:61:22: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcmp.c.pysam.c:89:30: style: Parameter 'vcmp' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/vcmp.c.pysam.c:94:15: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/vcmp.c.pysam.c:94:29: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/version.c:36:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCFTOOLS_VERSION [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:44:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:52:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:75:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_IDX_DELIM [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:88:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_IDX_DELIM [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:120:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_FMT_CSI [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:144:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vcf [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:174:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_FMT_CSI [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c:75:23: style: Condition 'fname' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/version.c:76:23: style: Condition 'fname' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/version.c:144:9: style: Condition 'idx_fmt' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/version.c:90:19: warning: Either the condition 'fname' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/version.c:89:23: note: Assuming that condition 'fname' is not redundant
pysam-0.23.0/bcftools/version.c:89:29: note: Assignment 'end=fname?fname+strlen(fname):fname', assigned value is 0
pysam-0.23.0/bcftools/version.c:90:19: note: Null pointer subtraction
pysam-0.23.0/bcftools/version.c:85:67: style:inconclusive: Function 'set_wmode' argument 4 names different: declaration 'compression_level' definition 'clevel'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bcftools.h:65:67: note: Function 'set_wmode' argument 4 names different: declaration 'compression_level' definition 'clevel'.
pysam-0.23.0/bcftools/version.c:85:67: note: Function 'set_wmode' argument 4 names different: declaration 'compression_level' definition 'clevel'.
pysam-0.23.0/bcftools/version.c:92:48: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/version.c:119:29: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/version.c:142:11: style: Variable 'idx_suffix' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/bcftools/version.c.pysam.c:38:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCFTOOLS_VERSION [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c.pysam.c:54:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c.pysam.c:77:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_IDX_DELIM [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c.pysam.c:90:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_IDX_DELIM [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c.pysam.c:122:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_FMT_CSI [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c.pysam.c:146:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vcf [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c.pysam.c:176:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_FMT_CSI [valueFlowBailoutIncompleteVar]
pysam-0.23.0/bcftools/version.c.pysam.c:77:23: style: Condition 'fname' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/version.c.pysam.c:78:23: style: Condition 'fname' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/version.c.pysam.c:146:9: style: Condition 'idx_fmt' is always true [knownConditionTrueFalse]
pysam-0.23.0/bcftools/version.c.pysam.c:92:19: warning: Either the condition 'fname' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
pysam-0.23.0/bcftools/version.c.pysam.c:91:23: note: Assuming that condition 'fname' is not redundant
pysam-0.23.0/bcftools/version.c.pysam.c:91:29: note: Assignment 'end=fname?fname+strlen(fname):fname', assigned value is 0
pysam-0.23.0/bcftools/version.c.pysam.c:92:19: note: Null pointer subtraction
pysam-0.23.0/bcftools/version.c.pysam.c:87:67: style:inconclusive: Function 'set_wmode' argument 4 names different: declaration 'compression_level' definition 'clevel'. [funcArgNamesDifferent]
pysam-0.23.0/bcftools/bcftools.h:65:67: note: Function 'set_wmode' argument 4 names different: declaration 'compression_level' definition 'clevel'.
pysam-0.23.0/bcftools/version.c.pysam.c:87:67: note: Function 'set_wmode' argument 4 names different: declaration 'compression_level' definition 'clevel'.
pysam-0.23.0/bcftools/version.c.pysam.c:94:48: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
pysam-0.23.0/bcftools/version.c.pysam.c:121:29: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/version.c.pysam.c:144:11: style: Variable 'idx_suffix' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/import/pysam.c:10:8: error: syntax error [syntaxError]
pysam-0.23.0/pysam/htslib_util.h:12:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/pysam/pysam_util.c:23:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFSIZ [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/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]
pysam-0.23.0/samtools/bam.c:72:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam.c:35:40: style:inconclusive: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam.h:32:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'.
pysam-0.23.0/samtools/bam.c:35:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'.
pysam-0.23.0/samtools/bam.c.pysam.c:74:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam.c.pysam.c:37:40: style:inconclusive: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam.h:32:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'.
pysam-0.23.0/samtools/bam.c.pysam.c:37:40: note: Function 'bam_get_library' argument 1 names different: declaration 'header' definition 'h'.
pysam-0.23.0/samtools/bam_color.c:54:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_color.c:83:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_color.c:144:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_color.c:43:11: style: Variable 'cs' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/bam_color.c:72:11: style: Variable 'cq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/bam_color.c.pysam.c:56:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_color.c.pysam.c:85:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_color.c.pysam.c:146:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_color.c.pysam.c:45:11: style: Variable 'cs' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/bam_color.c.pysam.c:74:11: style: Variable 'cq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/bam_lpileup.c:198:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c:197:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c:197:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c:198:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c:199:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c:197:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c:197:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c:199:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c:199:16: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c:197:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c:197:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c:199:16: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c:199:36: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c:197:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c:197:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c:199:36: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c:200:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c:197:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c:197:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c:200:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c:201:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c:197:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c:197:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c:201:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c:202:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c:197:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c:197:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c:202:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c:42:1: style:inconclusive: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam_lpileup.c:42:1: note: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c:42:1: note: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c:42:1: style:inconclusive: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam_lpileup.c:42:1: note: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c:42:1: note: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c:222:52: style:inconclusive: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam_lpileup.h:52:56: note: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'.
pysam-0.23.0/samtools/bam_lpileup.c:222:52: note: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'.
pysam-0.23.0/samtools/bam_lpileup.c:122:30: style: Local variable 'p' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_lpileup.c:106:17: note: Shadowed declaration
pysam-0.23.0/samtools/bam_lpileup.c:122:30: note: Shadow variable
pysam-0.23.0/samtools/bam_lpileup.c:125:29: style: Local variable 'p' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_lpileup.c:122:30: note: Shadowed declaration
pysam-0.23.0/samtools/bam_lpileup.c:125:29: note: Shadow variable
pysam-0.23.0/samtools/bam_lpileup.c:176:30: style: Local variable 'p' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_lpileup.c:106:17: note: Shadowed declaration
pysam-0.23.0/samtools/bam_lpileup.c:176:30: note: Shadow variable
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:200:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:200:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:201:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:201:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:201:16: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:201:16: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:201:36: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:201:36: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:202:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:202:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:203:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:203:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:204:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tv [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:31: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:199:10: note: Assignment 'tv=(struct bam_lplbuf_t*)calloc(1,sizeof(struct bam_lplbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:204:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:44:1: style:inconclusive: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:44:1: note: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:44:1: note: Function 'splay_flatten_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:44:1: style:inconclusive: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:44:1: note: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:44:1: note: Function 'splay_insert_node' argument 1 names different: declaration 'node' definition 'head'.
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:224:52: style:inconclusive: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/bam_lpileup.h:52:56: note: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'.
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:224:52: note: Function 'bam_lplbuf_push' argument 2 names different: declaration 'buf' definition 'tv'.
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:124:30: style: Local variable 'p' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:108:17: note: Shadowed declaration
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:124:30: note: Shadow variable
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:127:29: style: Local variable 'p' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:124:30: note: Shadowed declaration
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:127:29: note: Shadow variable
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:178:30: style: Local variable 'p' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:108:17: note: Shadowed declaration
pysam-0.23.0/samtools/bam_lpileup.c.pysam.c:178:30: note: Shadow variable
pysam-0.23.0/samtools/bam_plbuf.c:47:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_plbuf.c:46:17: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_plbuf.c:46:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_plbuf.c:47:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_plbuf.c:48:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_plbuf.c:46:17: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_plbuf.c:46:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_plbuf.c:48:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_plbuf.c:49:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_plbuf.c:46:17: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_plbuf.c:46:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_plbuf.c:49:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:49:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:48:17: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:48:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:49:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:50:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:48:17: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:48:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:50:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:51:5: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:48:17: note: Assuming allocation function fails
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:48:17: note: Assignment 'buf=calloc(1,sizeof(struct bam_plbuf_t))', assigned value is 0
pysam-0.23.0/samtools/bam_plbuf.c.pysam.c:51:5: note: Null pointer dereference
pysam-0.23.0/samtools/bam_quickcheck.c:82:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hts_verbose [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_quickcheck.c:157:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_quickcheck.c:119:9: note: Shadowed declaration
pysam-0.23.0/samtools/bam_quickcheck.c:157:17: note: Shadow variable
pysam-0.23.0/samtools/bam_quickcheck.c.pysam.c:84:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hts_verbose [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/bam_quickcheck.c.pysam.c:159:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
pysam-0.23.0/samtools/bam_quickcheck.c.pysam.c:121:9: note: Shadowed declaration
pysam-0.23.0/samtools/bam_quickcheck.c.pysam.c:159:17: note: Shadow variable
pysam-0.23.0/samtools/bam_samples.c:37:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/samtools/bam_samples.c.pysam.c:39:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/samtools/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]
pysam-0.23.0/samtools/bedidx.c.pysam.c:41:1: error: There is an unknown macro here somewhere. Configuration is required. If KSTREAM_INIT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/samtools/consensus_pileup.c:86:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CPAD [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/consensus_pileup.c:346:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/consensus_pileup.c:390:31: style: Condition 'phead' is always true [knownConditionTrueFalse]
pysam-0.23.0/samtools/consensus_pileup.c.pysam.c:88:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CPAD [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/consensus_pileup.c.pysam.c:360:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/consensus_pileup.c.pysam.c:392:31: style: Condition 'phead' is always true [knownConditionTrueFalse]
pysam-0.23.0/samtools/lz4/lz4.c:567:29: style:inconclusive: Boolean expression 'ip>anchor' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
pysam-0.23.0/samtools/lz4/lz4.c:1159:65: style:inconclusive: Boolean expression '(endOnInput?(ip<iend-((1U<<(8-4))-1)):1)!=0' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
pysam-0.23.0/samtools/lz4/lz4.c:943:14: warning: If memory allocation fails, then there is a possible null pointer dereference: LZ4_stream [nullPointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c:935:41: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c:935:26: note: Assignment 'lz4s=(union LZ4_stream_t*)calloc(8,(1<<(14-3))+4)', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c:937:21: note: Calling function 'LZ4_resetStream', 1st argument 'lz4s' value is 0
pysam-0.23.0/samtools/lz4/lz4.c:943:14: note: Null pointer dereference
pysam-0.23.0/samtools/lz4/lz4.c:1441:14: warning: If memory allocation fails, then there is a possible null pointer dereference: lz4ds [nullPointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c:1454:42: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c:1454:27: note: Assignment 'lz4ds=(union LZ4_stream_t*)calloc(8,sizeof(union LZ4_stream_t))', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c:1455:15: note: Calling function 'LZ4_init', 1st argument 'lz4ds' value is 0
pysam-0.23.0/samtools/lz4/lz4.c:1441:14: note: Null pointer dereference
pysam-0.23.0/samtools/lz4/lz4.c:1442:5: warning: If memory allocation fails, then there is a possible null pointer dereference: lz4ds [nullPointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c:1454:42: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c:1454:27: note: Assignment 'lz4ds=(union LZ4_stream_t*)calloc(8,sizeof(union LZ4_stream_t))', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c:1455:15: note: Calling function 'LZ4_init', 1st argument 'lz4ds' value is 0
pysam-0.23.0/samtools/lz4/lz4.c:1442:5: note: Null pointer dereference
pysam-0.23.0/samtools/lz4/lz4.c:413:27: style:inconclusive: Function 'LZ4_compressBound' argument 1 names different: declaration 'inputSize' definition 'isize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:165:38: note: Function 'LZ4_compressBound' argument 1 names different: declaration 'inputSize' definition 'isize'.
pysam-0.23.0/samtools/lz4/lz4.c:413:27: note: Function 'LZ4_compressBound' argument 1 names different: declaration 'inputSize' definition 'isize'.
pysam-0.23.0/samtools/lz4/lz4.c:677:96: style:inconclusive: Function 'LZ4_compress_fast_extState' argument 5 names different: declaration 'maxDestSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:186:108: note: Function 'LZ4_compress_fast_extState' argument 5 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:677:96: note: Function 'LZ4_compress_fast_extState' argument 5 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:697:59: style:inconclusive: Function 'LZ4_compress_fast' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:175:71: note: Function 'LZ4_compress_fast' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:697:59: note: Function 'LZ4_compress_fast' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:697:74: style:inconclusive: Function 'LZ4_compress_fast' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:175:87: note: Function 'LZ4_compress_fast' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:697:74: note: Function 'LZ4_compress_fast' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:715:62: style:inconclusive: Function 'LZ4_compress_default' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:135:73: note: Function 'LZ4_compress_default' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:715:62: note: Function 'LZ4_compress_default' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:715:77: style:inconclusive: Function 'LZ4_compress_default' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:135:89: note: Function 'LZ4_compress_default' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:715:77: note: Function 'LZ4_compress_default' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:910:39: style:inconclusive: Function 'LZ4_compress_destSize' argument 1 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:51: note: Function 'LZ4_compress_destSize' argument 1 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:910:39: note: Function 'LZ4_compress_destSize' argument 1 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:910:50: style:inconclusive: Function 'LZ4_compress_destSize' argument 2 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:65: note: Function 'LZ4_compress_destSize' argument 2 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:910:50: note: Function 'LZ4_compress_destSize' argument 2 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:910:60: style:inconclusive: Function 'LZ4_compress_destSize' argument 3 names different: declaration 'sourceSizePtr' definition 'srcSizePtr'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:76: note: Function 'LZ4_compress_destSize' argument 3 names different: declaration 'sourceSizePtr' definition 'srcSizePtr'.
pysam-0.23.0/samtools/lz4/lz4.c:910:60: note: Function 'LZ4_compress_destSize' argument 3 names different: declaration 'sourceSizePtr' definition 'srcSizePtr'.
pysam-0.23.0/samtools/lz4/lz4.c:910:76: style:inconclusive: Function 'LZ4_compress_destSize' argument 4 names different: declaration 'targetDestSize' definition 'targetDstSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:95: note: Function 'LZ4_compress_destSize' argument 4 names different: declaration 'targetDestSize' definition 'targetDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c:910:76: note: Function 'LZ4_compress_destSize' argument 4 names different: declaration 'targetDestSize' definition 'targetDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c:941:37: style:inconclusive: Function 'LZ4_resetStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:247:48: note: Function 'LZ4_resetStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:941:37: note: Function 'LZ4_resetStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:946:35: style:inconclusive: Function 'LZ4_freeStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:241:56: note: Function 'LZ4_freeStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:946:35: note: Function 'LZ4_freeStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:955:33: style:inconclusive: Function 'LZ4_loadDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:255:44: note: Function 'LZ4_loadDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c:955:33: note: Function 'LZ4_loadDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:47: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:58: note: Function 'LZ4_compress_fast_continue' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:47: note: Function 'LZ4_compress_fast_continue' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:71: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 2 names different: declaration 'src' definition 'source'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:81: note: Function 'LZ4_compress_fast_continue' argument 2 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:71: note: Function 'LZ4_compress_fast_continue' argument 2 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:85: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 3 names different: declaration 'dst' definition 'dest'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:92: note: Function 'LZ4_compress_fast_continue' argument 3 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:85: note: Function 'LZ4_compress_fast_continue' argument 3 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:95: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 4 names different: declaration 'srcSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:101: note: Function 'LZ4_compress_fast_continue' argument 4 names different: declaration 'srcSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:95: note: Function 'LZ4_compress_fast_continue' argument 4 names different: declaration 'srcSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:110: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 5 names different: declaration 'dstCapacity' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:114: note: Function 'LZ4_compress_fast_continue' argument 5 names different: declaration 'dstCapacity' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1006:110: note: Function 'LZ4_compress_fast_continue' argument 5 names different: declaration 'dstCapacity' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1081:33: style:inconclusive: Function 'LZ4_saveDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:273:44: note: Function 'LZ4_saveDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c:1081:33: note: Function 'LZ4_saveDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c:1325:129: style:inconclusive: Function 'LZ4_decompress_safe_continue' argument 5 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:310:140: note: Function 'LZ4_decompress_safe_continue' argument 5 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1325:129: note: Function 'LZ4_decompress_safe_continue' argument 5 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1397:91: style:inconclusive: Function 'LZ4_decompress_safe_usingDict' argument 4 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:319:103: note: Function 'LZ4_decompress_safe_usingDict' argument 4 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1397:91: note: Function 'LZ4_decompress_safe_usingDict' argument 4 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1418:68: style:inconclusive: Function 'LZ4_compress_limitedOutput' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:438:133: note: Function 'LZ4_compress_limitedOutput' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1418:68: note: Function 'LZ4_compress_limitedOutput' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1419:54: style:inconclusive: Function 'LZ4_compress' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:437:133: note: Function 'LZ4_compress' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1419:54: note: Function 'LZ4_compress' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:68: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 2 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:138: note: Function 'LZ4_compress_limitedOutput_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:68: note: Function 'LZ4_compress_limitedOutput_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:79: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 3 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:152: note: Function 'LZ4_compress_limitedOutput_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:79: note: Function 'LZ4_compress_limitedOutput_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:88: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:162: note: Function 'LZ4_compress_limitedOutput_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:88: note: Function 'LZ4_compress_limitedOutput_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:101: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 5 names different: declaration 'maxOutputSize' definition 'dstSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:177: note: Function 'LZ4_compress_limitedOutput_withState' argument 5 names different: declaration 'maxOutputSize' definition 'dstSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1420:101: note: Function 'LZ4_compress_limitedOutput_withState' argument 5 names different: declaration 'maxOutputSize' definition 'dstSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1421:54: style:inconclusive: Function 'LZ4_compress_withState' argument 2 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:439:138: note: Function 'LZ4_compress_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:1421:54: note: Function 'LZ4_compress_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:1421:65: style:inconclusive: Function 'LZ4_compress_withState' argument 3 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:439:152: note: Function 'LZ4_compress_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:1421:65: note: Function 'LZ4_compress_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:1421:74: style:inconclusive: Function 'LZ4_compress_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:439:162: note: Function 'LZ4_compress_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1421:74: note: Function 'LZ4_compress_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:56: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:127: note: Function 'LZ4_compress_limitedOutput_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:56: note: Function 'LZ4_compress_limitedOutput_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:80: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 2 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:154: note: Function 'LZ4_compress_limitedOutput_continue' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:80: note: Function 'LZ4_compress_limitedOutput_continue' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:91: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 3 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:168: note: Function 'LZ4_compress_limitedOutput_continue' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:91: note: Function 'LZ4_compress_limitedOutput_continue' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:100: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 4 names different: declaration 'inputSize' definition 'srcSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:178: note: Function 'LZ4_compress_limitedOutput_continue' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:100: note: Function 'LZ4_compress_limitedOutput_continue' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:113: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 5 names different: declaration 'maxOutputSize' definition 'maxDstSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:193: note: Function 'LZ4_compress_limitedOutput_continue' argument 5 names different: declaration 'maxOutputSize' definition 'maxDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1422:113: note: Function 'LZ4_compress_limitedOutput_continue' argument 5 names different: declaration 'maxOutputSize' definition 'maxDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1423:42: style:inconclusive: Function 'LZ4_compress_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:441:127: note: Function 'LZ4_compress_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:1423:42: note: Function 'LZ4_compress_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c:1459:35: style:inconclusive: Function 'LZ4_slideInputBuffer' argument 1 names different: declaration 'state' definition 'LZ4_Data'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:452:95: note: Function 'LZ4_slideInputBuffer' argument 1 names different: declaration 'state' definition 'LZ4_Data'.
pysam-0.23.0/samtools/lz4/lz4.c:1459:35: note: Function 'LZ4_slideInputBuffer' argument 1 names different: declaration 'state' definition 'LZ4_Data'.
pysam-0.23.0/samtools/lz4/lz4.c:1468:51: style:inconclusive: Function 'LZ4_decompress_safe_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:455:125: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c:1468:51: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c:1468:65: style:inconclusive: Function 'LZ4_decompress_safe_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:455:136: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c:1468:65: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c:1468:95: style:inconclusive: Function 'LZ4_decompress_safe_withPrefix64k' argument 4 names different: declaration 'maxDstSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:455:165: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 4 names different: declaration 'maxDstSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1468:95: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 4 names different: declaration 'maxDstSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c:1473:51: style:inconclusive: Function 'LZ4_decompress_fast_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:456:125: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c:1473:51: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c:1473:65: style:inconclusive: Function 'LZ4_decompress_fast_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:456:136: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c:1473:65: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c:260:17: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:502:17: style: Variable 'olimit' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:756:17: style: Variable 'oend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:757:17: style: Variable 'oMaxLit' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:758:17: style: Variable 'oMaxMatch' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:759:17: style: Variable 'oMaxSeq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:1128:17: style: Variable 'oend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:1218:33: style: Variable 'endOfMatch' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c:171:23: style: union member 'Anonymous0::u' is never used. [unusedStructMember]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:569:29: style:inconclusive: Boolean expression 'ip>anchor' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1161:65: style:inconclusive: Boolean expression '(endOnInput?(ip<iend-((1U<<(8-4))-1)):1)!=0' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:945:14: warning: If memory allocation fails, then there is a possible null pointer dereference: LZ4_stream [nullPointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:937:41: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:937:26: note: Assignment 'lz4s=(union LZ4_stream_t*)calloc(8,(1<<(14-3))+4)', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:939:21: note: Calling function 'LZ4_resetStream', 1st argument 'lz4s' value is 0
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:945:14: note: Null pointer dereference
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1443:14: warning: If memory allocation fails, then there is a possible null pointer dereference: lz4ds [nullPointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1456:42: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1456:27: note: Assignment 'lz4ds=(union LZ4_stream_t*)calloc(8,sizeof(union LZ4_stream_t))', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1457:15: note: Calling function 'LZ4_init', 1st argument 'lz4ds' value is 0
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1443:14: note: Null pointer dereference
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1444:5: warning: If memory allocation fails, then there is a possible null pointer dereference: lz4ds [nullPointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1456:42: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1456:27: note: Assignment 'lz4ds=(union LZ4_stream_t*)calloc(8,sizeof(union LZ4_stream_t))', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1457:15: note: Calling function 'LZ4_init', 1st argument 'lz4ds' value is 0
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1444:5: note: Null pointer dereference
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:415:27: style:inconclusive: Function 'LZ4_compressBound' argument 1 names different: declaration 'inputSize' definition 'isize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:165:38: note: Function 'LZ4_compressBound' argument 1 names different: declaration 'inputSize' definition 'isize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:415:27: note: Function 'LZ4_compressBound' argument 1 names different: declaration 'inputSize' definition 'isize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:679:96: style:inconclusive: Function 'LZ4_compress_fast_extState' argument 5 names different: declaration 'maxDestSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:186:108: note: Function 'LZ4_compress_fast_extState' argument 5 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:679:96: note: Function 'LZ4_compress_fast_extState' argument 5 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:699:59: style:inconclusive: Function 'LZ4_compress_fast' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:175:71: note: Function 'LZ4_compress_fast' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:699:59: note: Function 'LZ4_compress_fast' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:699:74: style:inconclusive: Function 'LZ4_compress_fast' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:175:87: note: Function 'LZ4_compress_fast' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:699:74: note: Function 'LZ4_compress_fast' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:717:62: style:inconclusive: Function 'LZ4_compress_default' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:135:73: note: Function 'LZ4_compress_default' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:717:62: note: Function 'LZ4_compress_default' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:717:77: style:inconclusive: Function 'LZ4_compress_default' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:135:89: note: Function 'LZ4_compress_default' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:717:77: note: Function 'LZ4_compress_default' argument 4 names different: declaration 'maxDestSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:39: style:inconclusive: Function 'LZ4_compress_destSize' argument 1 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:51: note: Function 'LZ4_compress_destSize' argument 1 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:39: note: Function 'LZ4_compress_destSize' argument 1 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:50: style:inconclusive: Function 'LZ4_compress_destSize' argument 2 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:65: note: Function 'LZ4_compress_destSize' argument 2 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:50: note: Function 'LZ4_compress_destSize' argument 2 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:60: style:inconclusive: Function 'LZ4_compress_destSize' argument 3 names different: declaration 'sourceSizePtr' definition 'srcSizePtr'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:76: note: Function 'LZ4_compress_destSize' argument 3 names different: declaration 'sourceSizePtr' definition 'srcSizePtr'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:60: note: Function 'LZ4_compress_destSize' argument 3 names different: declaration 'sourceSizePtr' definition 'srcSizePtr'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:76: style:inconclusive: Function 'LZ4_compress_destSize' argument 4 names different: declaration 'targetDestSize' definition 'targetDstSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:200:95: note: Function 'LZ4_compress_destSize' argument 4 names different: declaration 'targetDestSize' definition 'targetDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:912:76: note: Function 'LZ4_compress_destSize' argument 4 names different: declaration 'targetDestSize' definition 'targetDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:943:37: style:inconclusive: Function 'LZ4_resetStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:247:48: note: Function 'LZ4_resetStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:943:37: note: Function 'LZ4_resetStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:948:35: style:inconclusive: Function 'LZ4_freeStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:241:56: note: Function 'LZ4_freeStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:948:35: note: Function 'LZ4_freeStream' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:957:33: style:inconclusive: Function 'LZ4_loadDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:255:44: note: Function 'LZ4_loadDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:957:33: note: Function 'LZ4_loadDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:47: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:58: note: Function 'LZ4_compress_fast_continue' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:47: note: Function 'LZ4_compress_fast_continue' argument 1 names different: declaration 'streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:71: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 2 names different: declaration 'src' definition 'source'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:81: note: Function 'LZ4_compress_fast_continue' argument 2 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:71: note: Function 'LZ4_compress_fast_continue' argument 2 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:85: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 3 names different: declaration 'dst' definition 'dest'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:92: note: Function 'LZ4_compress_fast_continue' argument 3 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:85: note: Function 'LZ4_compress_fast_continue' argument 3 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:95: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 4 names different: declaration 'srcSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:101: note: Function 'LZ4_compress_fast_continue' argument 4 names different: declaration 'srcSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:95: note: Function 'LZ4_compress_fast_continue' argument 4 names different: declaration 'srcSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:110: style:inconclusive: Function 'LZ4_compress_fast_continue' argument 5 names different: declaration 'dstCapacity' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:265:114: note: Function 'LZ4_compress_fast_continue' argument 5 names different: declaration 'dstCapacity' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1008:110: note: Function 'LZ4_compress_fast_continue' argument 5 names different: declaration 'dstCapacity' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1083:33: style:inconclusive: Function 'LZ4_saveDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:273:44: note: Function 'LZ4_saveDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1083:33: note: Function 'LZ4_saveDict' argument 1 names different: declaration 'streamPtr' definition 'LZ4_dict'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1327:129: style:inconclusive: Function 'LZ4_decompress_safe_continue' argument 5 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:310:140: note: Function 'LZ4_decompress_safe_continue' argument 5 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1327:129: note: Function 'LZ4_decompress_safe_continue' argument 5 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1399:91: style:inconclusive: Function 'LZ4_decompress_safe_usingDict' argument 4 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:319:103: note: Function 'LZ4_decompress_safe_usingDict' argument 4 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1399:91: note: Function 'LZ4_decompress_safe_usingDict' argument 4 names different: declaration 'maxDecompressedSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1420:68: style:inconclusive: Function 'LZ4_compress_limitedOutput' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:438:133: note: Function 'LZ4_compress_limitedOutput' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1420:68: note: Function 'LZ4_compress_limitedOutput' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1421:54: style:inconclusive: Function 'LZ4_compress' argument 3 names different: declaration 'sourceSize' definition 'inputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:437:133: note: Function 'LZ4_compress' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1421:54: note: Function 'LZ4_compress' argument 3 names different: declaration 'sourceSize' definition 'inputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:68: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 2 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:138: note: Function 'LZ4_compress_limitedOutput_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:68: note: Function 'LZ4_compress_limitedOutput_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:79: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 3 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:152: note: Function 'LZ4_compress_limitedOutput_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:79: note: Function 'LZ4_compress_limitedOutput_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:88: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:162: note: Function 'LZ4_compress_limitedOutput_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:88: note: Function 'LZ4_compress_limitedOutput_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:101: style:inconclusive: Function 'LZ4_compress_limitedOutput_withState' argument 5 names different: declaration 'maxOutputSize' definition 'dstSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:440:177: note: Function 'LZ4_compress_limitedOutput_withState' argument 5 names different: declaration 'maxOutputSize' definition 'dstSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1422:101: note: Function 'LZ4_compress_limitedOutput_withState' argument 5 names different: declaration 'maxOutputSize' definition 'dstSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1423:54: style:inconclusive: Function 'LZ4_compress_withState' argument 2 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:439:138: note: Function 'LZ4_compress_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1423:54: note: Function 'LZ4_compress_withState' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1423:65: style:inconclusive: Function 'LZ4_compress_withState' argument 3 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:439:152: note: Function 'LZ4_compress_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1423:65: note: Function 'LZ4_compress_withState' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1423:74: style:inconclusive: Function 'LZ4_compress_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:439:162: note: Function 'LZ4_compress_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1423:74: note: Function 'LZ4_compress_withState' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:56: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:127: note: Function 'LZ4_compress_limitedOutput_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:56: note: Function 'LZ4_compress_limitedOutput_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:80: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 2 names different: declaration 'source' definition 'src'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:154: note: Function 'LZ4_compress_limitedOutput_continue' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:80: note: Function 'LZ4_compress_limitedOutput_continue' argument 2 names different: declaration 'source' definition 'src'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:91: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 3 names different: declaration 'dest' definition 'dst'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:168: note: Function 'LZ4_compress_limitedOutput_continue' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:91: note: Function 'LZ4_compress_limitedOutput_continue' argument 3 names different: declaration 'dest' definition 'dst'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:100: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 4 names different: declaration 'inputSize' definition 'srcSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:178: note: Function 'LZ4_compress_limitedOutput_continue' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:100: note: Function 'LZ4_compress_limitedOutput_continue' argument 4 names different: declaration 'inputSize' definition 'srcSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:113: style:inconclusive: Function 'LZ4_compress_limitedOutput_continue' argument 5 names different: declaration 'maxOutputSize' definition 'maxDstSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:442:193: note: Function 'LZ4_compress_limitedOutput_continue' argument 5 names different: declaration 'maxOutputSize' definition 'maxDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1424:113: note: Function 'LZ4_compress_limitedOutput_continue' argument 5 names different: declaration 'maxOutputSize' definition 'maxDstSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1425:42: style:inconclusive: Function 'LZ4_compress_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:441:127: note: Function 'LZ4_compress_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1425:42: note: Function 'LZ4_compress_continue' argument 1 names different: declaration 'LZ4_streamPtr' definition 'LZ4_stream'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1461:35: style:inconclusive: Function 'LZ4_slideInputBuffer' argument 1 names different: declaration 'state' definition 'LZ4_Data'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:452:95: note: Function 'LZ4_slideInputBuffer' argument 1 names different: declaration 'state' definition 'LZ4_Data'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1461:35: note: Function 'LZ4_slideInputBuffer' argument 1 names different: declaration 'state' definition 'LZ4_Data'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1470:51: style:inconclusive: Function 'LZ4_decompress_safe_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:455:125: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1470:51: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1470:65: style:inconclusive: Function 'LZ4_decompress_safe_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:455:136: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1470:65: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1470:95: style:inconclusive: Function 'LZ4_decompress_safe_withPrefix64k' argument 4 names different: declaration 'maxDstSize' definition 'maxOutputSize'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:455:165: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 4 names different: declaration 'maxDstSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1470:95: note: Function 'LZ4_decompress_safe_withPrefix64k' argument 4 names different: declaration 'maxDstSize' definition 'maxOutputSize'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1475:51: style:inconclusive: Function 'LZ4_decompress_fast_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:456:125: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1475:51: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 1 names different: declaration 'src' definition 'source'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1475:65: style:inconclusive: Function 'LZ4_decompress_fast_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'. [funcArgNamesDifferent]
pysam-0.23.0/samtools/lz4/lz4.h:456:136: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1475:65: note: Function 'LZ4_decompress_fast_withPrefix64k' argument 2 names different: declaration 'dst' definition 'dest'.
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:262:17: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:504:17: style: Variable 'olimit' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:758:17: style: Variable 'oend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:759:17: style: Variable 'oMaxLit' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:760:17: style: Variable 'oMaxMatch' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:761:17: style: Variable 'oMaxSeq' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1130:17: style: Variable 'oend' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1220:33: style: Variable 'endOfMatch' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:173:23: style: union member 'Anonymous0::u' is never used. [unusedStructMember]
pysam-0.23.0/samtools/sam_opts.c:71:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/sam_opts.c:140:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/sam_opts.c:111:18: style: Variable 'opts' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/sam_opts.c.pysam.c:99:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hts_verbose [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/sam_opts.c.pysam.c:142:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/sam_opts.c.pysam.c:113:18: style: Variable 'opts' can be declared as pointer to const [constVariablePointer]
pysam-0.23.0/samtools/sample.c:32:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/samtools/sample.c.pysam.c:34:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
pysam-0.23.0/samtools/samtools.pysam.c:54:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/samtools.pysam.c:70:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/stats_isize.h:41:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro]
pysam-0.23.0/samtools/tmp_file.c:67:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c:115:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c:195:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c:253:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c:382:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c:109:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/samtools/tmp_file.c:251:45: style: Parameter 'inbam' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/samtools/tmp_file.c.pysam.c:69:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c.pysam.c:117:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c.pysam.c:197:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c.pysam.c:255:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c.pysam.c:384:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam1_t [valueFlowBailoutIncompleteVar]
pysam-0.23.0/samtools/tmp_file.c.pysam.c:111:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
pysam-0.23.0/samtools/tmp_file.c.pysam.c:253:45: style: Parameter 'inbam' can be declared as pointer to const [constParameterPointer]
pysam-0.23.0/bcftools/HMM.c:95:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:20: note: Calling function hmm_init_states, 1st argument is null
pysam-0.23.0/bcftools/HMM.c:95:5: note: Dereferencing argument hmm that is null
pysam-0.23.0/bcftools/HMM.c:191:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:18: note: Calling function hmm_set_tprob, 1st argument is null
pysam-0.23.0/bcftools/HMM.c:191:5: note: Dereferencing argument hmm that is null
pysam-0.23.0/bcftools/HMM.c.pysam.c:97:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:135:20: note: Calling function hmm_init_states, 1st argument is null
pysam-0.23.0/bcftools/HMM.c.pysam.c:97:5: note: Dereferencing argument hmm that is null
pysam-0.23.0/bcftools/HMM.c.pysam.c:193:5: warning: If memory allocation fails, then there is a possible null pointer dereference: hmm [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/HMM.c:130:33: note: Assuming allocation function fails
pysam-0.23.0/bcftools/HMM.c:130:18: note: Assignment 'hmm=(struct hmm_t*)calloc(1,sizeof(struct hmm_t))', assigned value is 0
pysam-0.23.0/bcftools/HMM.c:134:18: note: Calling function hmm_set_tprob, 1st argument is null
pysam-0.23.0/bcftools/HMM.c.pysam.c:193:5: note: Dereferencing argument hmm that is null
pysam-0.23.0/bcftools/extsort.c:49:1: error: Null pointer dereference: dat [ctunullpointer]
pysam-0.23.0/bcftools/extsort.c:49:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/extsort.c:49:1: note: Dereferencing argument dat that is null
pysam-0.23.0/bcftools/extsort.c:65:17: error: Null pointer dereference: aptr [ctunullpointer]
pysam-0.23.0/bcftools/extsort.c:49:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/extsort.c:49:1: note: Calling function blk_is_smaller, 1st argument is null
pysam-0.23.0/bcftools/extsort.c:65:17: note: Dereferencing argument aptr that is null
pysam-0.23.0/bcftools/extsort.c.pysam.c:51:1: error: Null pointer dereference: dat [ctunullpointer]
pysam-0.23.0/bcftools/extsort.c.pysam.c:51:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/extsort.c.pysam.c:51:1: note: Dereferencing argument dat that is null
pysam-0.23.0/bcftools/extsort.c.pysam.c:67:17: error: Null pointer dereference: aptr [ctunullpointer]
pysam-0.23.0/bcftools/extsort.c.pysam.c:51:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/extsort.c.pysam.c:51:1: note: Calling function blk_is_smaller, 1st argument is null
pysam-0.23.0/bcftools/extsort.c.pysam.c:67:17: note: Dereferencing argument aptr that is null
pysam-0.23.0/bcftools/hclust.c:58:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c:128:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c:128:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c:135:46: note: Calling function append_node, 1st argument is null
pysam-0.23.0/bcftools/hclust.c:58:5: note: Dereferencing argument clust that is null
pysam-0.23.0/bcftools/hclust.c.pysam.c:60:5: warning: If memory allocation fails, then there is a possible null pointer dereference: clust [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:41: note: Assuming allocation function fails
pysam-0.23.0/bcftools/hclust.c.pysam.c:130:23: note: Assignment 'clust=(struct hclust_t*)calloc(1,sizeof(struct hclust_t))', assigned value is 0
pysam-0.23.0/bcftools/hclust.c.pysam.c:137:46: note: Calling function append_node, 1st argument is null
pysam-0.23.0/bcftools/hclust.c.pysam.c:60:5: note: Dereferencing argument clust that is null
pysam-0.23.0/bcftools/prob1.c:42:21: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:112:23: note: Calling function 'bcf_p1_init_prior', 1st argument 'ma' value is 0
pysam-0.23.0/bcftools/prob1.c:67:23: note: Calling function bcf_p1_indel_prior, 1st argument is null
pysam-0.23.0/bcftools/prob1.c:42:21: note: Dereferencing argument ma that is null
pysam-0.23.0/bcftools/prob1.c:66:29: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:112:22: note: Calling function bcf_p1_init_prior, 1st argument is null
pysam-0.23.0/bcftools/prob1.c:66:29: note: Dereferencing argument ma that is null
pysam-0.23.0/bcftools/prob1.c.pysam.c:44:21: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c.pysam.c:85:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:114:23: note: Calling function 'bcf_p1_init_prior', 1st argument 'ma' value is 0
pysam-0.23.0/bcftools/prob1.c.pysam.c:69:23: note: Calling function bcf_p1_indel_prior, 1st argument is null
pysam-0.23.0/bcftools/prob1.c.pysam.c:44:21: note: Dereferencing argument ma that is null
pysam-0.23.0/bcftools/prob1.c.pysam.c:68:29: warning: If memory allocation fails, then there is a possible null pointer dereference: ma [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/prob1.c:83:31: note: Assuming allocation function fails
pysam-0.23.0/bcftools/prob1.c:83:10: note: Assignment 'ma=(struct bcf_p1aux_t*)calloc(1,sizeof(struct bcf_p1aux_t))', assigned value is 0
pysam-0.23.0/bcftools/prob1.c:112:22: note: Calling function bcf_p1_init_prior, 1st argument is null
pysam-0.23.0/bcftools/prob1.c.pysam.c:68:29: note: Dereferencing argument ma that is null
pysam-0.23.0/bcftools/read_consensus.c:72:10: error: Null pointer dereference: a [ctunullpointer]
pysam-0.23.0/bcftools/read_consensus.c:75:1: note: Calling function khp_heapify_cvh, 2nd argument is null
pysam-0.23.0/bcftools/read_consensus.c:75:1: note: Calling function cvar_not_preferred, 1st argument is null
pysam-0.23.0/bcftools/read_consensus.c:72:10: note: Dereferencing argument a that is null
pysam-0.23.0/bcftools/read_consensus.c:75:1: error: Null pointer dereference: dat [ctunullpointer]
pysam-0.23.0/bcftools/read_consensus.c:75:1: note: Calling function khp_heapify_cvh, 2nd argument is null
pysam-0.23.0/bcftools/read_consensus.c:75:1: note: Dereferencing argument dat that is null
pysam-0.23.0/bcftools/read_consensus.c:121:17: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c:218:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c:218:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c:223:21: note: Calling function init_arrays, 1st argument is null
pysam-0.23.0/bcftools/read_consensus.c:121:17: note: Dereferencing argument rcns that is null
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:74:10: error: Null pointer dereference: a [ctunullpointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:77:1: note: Calling function khp_heapify_cvh, 2nd argument is null
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:77:1: note: Calling function cvar_not_preferred, 1st argument is null
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:74:10: note: Dereferencing argument a that is null
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:77:1: error: Null pointer dereference: dat [ctunullpointer]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:77:1: note: Calling function khp_heapify_cvh, 2nd argument is null
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:77:1: note: Dereferencing argument dat that is null
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:123:17: warning: If memory allocation fails, then there is a possible null pointer dereference: rcns [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:44: note: Assuming allocation function fails
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:220:24: note: Assignment 'rcns=(struct read_cns_t*)calloc(1,sizeof(struct read_cns_t))', assigned value is 0
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:225:21: note: Calling function init_arrays, 1st argument is null
pysam-0.23.0/bcftools/read_consensus.c.pysam.c:123:17: note: Dereferencing argument rcns that is null
pysam-0.23.0/bcftools/vcfgtcheck.c:101:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c:1195:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c:1196:52: note: Calling function set_cwd, 1st argument is null
pysam-0.23.0/bcftools/vcfgtcheck.c:101:5: note: Dereferencing argument args that is null
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:103:5: warning: If memory allocation fails, then there is a possible null pointer dereference: args [ctunullpointerOutOfMemory]
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:36: note: Assuming allocation function fails
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1197:20: note: Assignment 'args=(struct args_t*)calloc(1,sizeof(struct args_t))', assigned value is 0
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:1198:52: note: Calling function set_cwd, 1st argument is null
pysam-0.23.0/bcftools/vcfgtcheck.c.pysam.c:103:5: note: Dereferencing argument args that is null
pysam-0.23.0/bcftools/vcfsort.c:522:17: error: Null pointer dereference: aptr [ctunullpointer]
pysam-0.23.0/bcftools/vcfsort.c:529:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/vcfsort.c:529:1: note: Calling function blk_is_smaller, 1st argument is null
pysam-0.23.0/bcftools/vcfsort.c:522:17: note: Dereferencing argument aptr that is null
pysam-0.23.0/bcftools/vcfsort.c:529:1: error: Null pointer dereference: dat [ctunullpointer]
pysam-0.23.0/bcftools/vcfsort.c:529:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/vcfsort.c:529:1: note: Dereferencing argument dat that is null
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:524:17: error: Null pointer dereference: aptr [ctunullpointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:531:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:531:1: note: Calling function blk_is_smaller, 1st argument is null
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:524:17: note: Dereferencing argument aptr that is null
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:531:1: error: Null pointer dereference: dat [ctunullpointer]
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:531:1: note: Calling function khp_heapify_blk, 2nd argument is null
pysam-0.23.0/bcftools/vcfsort.c.pysam.c:531:1: note: Dereferencing argument dat that is null
pysam-0.23.0/bcftools/vcfstats.c:639:20: error: Null pointer dereference: reader [ctunullpointer]
pysam-0.23.0/bcftools/vcfstats.c:1248:28: note: Assignment 'reader=NULL', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c:1251:20: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfstats.c:1271:17: note: Calling function init_iaf, 2nd argument is null
pysam-0.23.0/bcftools/vcfstats.c:639:20: note: Dereferencing argument reader that is null
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:641:20: error: Null pointer dereference: reader [ctunullpointer]
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1250:28: note: Assignment 'reader=NULL', assigned value is 0
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1253:20: note: Assuming condition is false
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:1273:17: note: Calling function init_iaf, 2nd argument is null
pysam-0.23.0/bcftools/vcfstats.c.pysam.c:641:20: note: Dereferencing argument reader that is null
pysam-0.23.0/samtools/lz4/lz4.c:943:14: warning: If memory allocation fails, then there is a possible null pointer dereference: LZ4_stream [ctunullpointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c:935:41: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c:935:26: note: Assignment 'lz4s=(union LZ4_stream_t*)calloc(8,(1<<(14-3))+4)', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c:937:20: note: Calling function LZ4_resetStream, 1st argument is null
pysam-0.23.0/samtools/lz4/lz4.c:943:14: note: Dereferencing argument LZ4_stream that is null
pysam-0.23.0/samtools/lz4/lz4.c:1441:14: warning: If memory allocation fails, then there is a possible null pointer dereference: lz4ds [ctunullpointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c:1454:42: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c:1454:27: note: Assignment 'lz4ds=(union LZ4_stream_t*)calloc(8,sizeof(union LZ4_stream_t))', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c:1455:14: note: Calling function LZ4_init, 1st argument is null
pysam-0.23.0/samtools/lz4/lz4.c:1441:14: note: Dereferencing argument lz4ds that is null
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:945:14: warning: If memory allocation fails, then there is a possible null pointer dereference: LZ4_stream [ctunullpointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c:935:41: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c:935:26: note: Assignment 'lz4s=(union LZ4_stream_t*)calloc(8,(1<<(14-3))+4)', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c:937:20: note: Calling function LZ4_resetStream, 1st argument is null
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:945:14: note: Dereferencing argument LZ4_stream that is null
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1443:14: warning: If memory allocation fails, then there is a possible null pointer dereference: lz4ds [ctunullpointerOutOfMemory]
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1456:42: note: Assuming allocation function fails
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1456:27: note: Assignment 'lz4ds=(union LZ4_stream_t*)calloc(8,sizeof(union LZ4_stream_t))', assigned value is 0
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1457:14: note: Calling function LZ4_init, 1st argument is null
pysam-0.23.0/samtools/lz4/lz4.c.pysam.c:1443:14: note: Dereferencing argument lz4ds that is null
diff:


DONE