2025-05-09 03:38
ftp://ftp.de.debian.org/debian/pool/main/a/abpoa/abpoa_1.5.3.orig.tar.gz
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 -j3
platform: Linux-6.8.0-1022-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: 66c9938 (2025-05-08 13:55:11 +0200)
count: 281 281
elapsed-time: 100.4 104.9
head-timing-info:

old-timing-info:

head results:
abPOA-1.5.3/include/simd_instruction.h:619:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/example.c:125:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_instruction.h:619:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.h:28:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.h:33:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.h:38:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.h:43:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.h:48:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.h:53:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.h:45:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.h:59:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.h:80:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.h:117:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa.c:146:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa.c:162:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/include/simd_instruction.h:623:9: portability: %ld in format string (no. 2) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
abPOA-1.5.3/example.c:114:9: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/example.c:110:33: note: Assuming allocation function fails
abPOA-1.5.3/example.c:110:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/example.c:114:9: note: Null pointer dereference
abPOA-1.5.3/example.c:115:9: warning: If memory allocation fails, then there is a possible null pointer dereference: bseqs [nullPointerOutOfMemory]
abPOA-1.5.3/example.c:111:40: note: Assuming allocation function fails
abPOA-1.5.3/example.c:111:23: note: Assignment 'bseqs=(uint8_t**)malloc(sizeof(uint8_t*)*n_seqs)', assigned value is 0
abPOA-1.5.3/example.c:115:9: note: Null pointer dereference
abPOA-1.5.3/example.c:115:55: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/example.c:110:33: note: Assuming allocation function fails
abPOA-1.5.3/example.c:110:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/example.c:115:55: note: Null pointer dereference
abPOA-1.5.3/example.c:116:9: warning: If memory allocation fails, then there is a possible null pointer dereference: weights [nullPointerOutOfMemory]
abPOA-1.5.3/example.c:112:34: note: Assuming allocation function fails
abPOA-1.5.3/example.c:112:21: note: Assignment 'weights=(int**)malloc(sizeof(int*)*n_seqs)', assigned value is 0
abPOA-1.5.3/example.c:116:9: note: Null pointer dereference
abPOA-1.5.3/example.c:116:49: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/example.c:110:33: note: Assuming allocation function fails
abPOA-1.5.3/example.c:110:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/example.c:116:49: note: Null pointer dereference
abPOA-1.5.3/example.c:117:25: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/example.c:110:33: note: Assuming allocation function fails
abPOA-1.5.3/example.c:110:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/example.c:117:25: note: Null pointer dereference
abPOA-1.5.3/example.c:118:13: warning: If memory allocation fails, then there is a possible null pointer dereference: bseqs [nullPointerOutOfMemory]
abPOA-1.5.3/example.c:111:40: note: Assuming allocation function fails
abPOA-1.5.3/example.c:111:23: note: Assignment 'bseqs=(uint8_t**)malloc(sizeof(uint8_t*)*n_seqs)', assigned value is 0
abPOA-1.5.3/example.c:118:13: note: Null pointer dereference
abPOA-1.5.3/example.c:69:10: style: Variable 'seqs' can be declared as const array [constVariable]
abPOA-1.5.3/example.c:132:19: style: Variable 'abc' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_align.c:48:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.c:62:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.c:118:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.c:203:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.c:304:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.c:390:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.c:438:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:13:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:48:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:85:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:190:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:236:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:281:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:319:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:370:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:389:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:420:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:487:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:582:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:603:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:696:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_instruction.h:623:9: portability: %ld in format string (no. 2) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
abPOA-1.5.3/src/abpoa_seq.h:7:1: warning: If memory allocation fails, then there is a possible null pointer dereference: ks [nullPointerOutOfMemory]
abPOA-1.5.3/src/abpoa_seq.h:7:1: note: Assuming allocation function fails
abPOA-1.5.3/src/abpoa_seq.h:7:1: note: Assignment 'ks=(struct kstream_t*)calloc(1,sizeof(struct kstream_t))', assigned value is 0
abPOA-1.5.3/src/abpoa_seq.h:7:1: note: Null pointer dereference
abPOA-1.5.3/src/abpoa_seq.h:7:1: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
abPOA-1.5.3/src/abpoa_seq.h:7:1: note: Assuming allocation function fails
abPOA-1.5.3/src/abpoa_seq.h:7:1: note: Assignment 's=(struct kseq_t*)calloc(1,sizeof(struct kseq_t))', assigned value is 0
abPOA-1.5.3/src/abpoa_seq.h:7:1: note: Null pointer dereference
abPOA-1.5.3/src/abpoa.c:144:48: warning: If resource allocation fails, then there is a possible null pointer dereference: list_fp [nullPointerOutOfResources]
abPOA-1.5.3/src/abpoa.c:143:30: note: Assuming allocation function fails
abPOA-1.5.3/src/abpoa.c:143:30: note: Assignment 'list_fp=fopen(file_fn,"r")', assigned value is 0
abPOA-1.5.3/src/abpoa.c:144:48: note: Null pointer dereference
abPOA-1.5.3/src/abpoa_align.h:75:140: style: Parameter 'src_cigar' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_align.h:98:66: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:63:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:175:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:271:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:431:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:440:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:510:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:581:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:600:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:732:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:773:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:781:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:851:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:919:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:950:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_align.c:179:75: style:inconclusive: Function 'abpoa_align_sequence_to_subgraph' argument 3 names different: declaration 'beg_node_id' definition 'exc_beg_node_id'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:168:75: note: Function 'abpoa_align_sequence_to_subgraph' argument 3 names different: declaration 'beg_node_id' definition 'exc_beg_node_id'.
abPOA-1.5.3/src/abpoa_align.c:179:75: note: Function 'abpoa_align_sequence_to_subgraph' argument 3 names different: declaration 'beg_node_id' definition 'exc_beg_node_id'.
abPOA-1.5.3/src/abpoa_align.c:179:96: style:inconclusive: Function 'abpoa_align_sequence_to_subgraph' argument 4 names different: declaration 'end_node_id' definition 'exc_end_node_id'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:168:92: note: Function 'abpoa_align_sequence_to_subgraph' argument 4 names different: declaration 'end_node_id' definition 'exc_end_node_id'.
abPOA-1.5.3/src/abpoa_align.c:179:96: note: Function 'abpoa_align_sequence_to_subgraph' argument 4 names different: declaration 'end_node_id' definition 'exc_end_node_id'.
abPOA-1.5.3/src/abpoa_align.c:365:52: style:inconclusive: Function 'abpoa_msa' argument 3 names different: declaration 'n_seqs' definition 'n_seq'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:153:52: note: Function 'abpoa_msa' argument 3 names different: declaration 'n_seqs' definition 'n_seq'.
abPOA-1.5.3/src/abpoa_align.c:365:52: note: Function 'abpoa_msa' argument 3 names different: declaration 'n_seqs' definition 'n_seq'.
abPOA-1.5.3/src/abpoa_align.c:226:34: style: Local variable 'tmp' shadows outer variable [shadowVariable]
abPOA-1.5.3/src/abpoa_align.c:197:10: note: Shadowed declaration
abPOA-1.5.3/src/abpoa_align.c:226:34: note: Shadow variable
abPOA-1.5.3/src/abpoa_align.c:241:34: style: Local variable 'tmp' shadows outer variable [shadowVariable]
abPOA-1.5.3/src/abpoa_align.c:197:10: note: Shadowed declaration
abPOA-1.5.3/src/abpoa_align.c:241:34: note: Shadow variable
abPOA-1.5.3/src/abpoa_align.c:448:17: style: Local variable 'ab_char26_table' shadows outer variable [shadowVariable]
abPOA-1.5.3/src/abpoa_align.c:31:13: note: Shadowed declaration
abPOA-1.5.3/src/abpoa_align.c:448:17: note: Shadow variable
abPOA-1.5.3/src/abpoa_align.c:42:41: style: Parameter 'order' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_align.c:193:91: style: Parameter 'seq_lens' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_align.c:193:128: style: Parameter 'par_c' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_align.c:193:184: style: Parameter 'read_id_map' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_align.c:296:84: style: Parameter 'seq_lens' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_align.c:431:55: style: Parameter 'read_fn' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_align.c:195:58: style: Variable 'm_c' is assigned a value that is never used. [unreadVariable]
abPOA-1.5.3/src/abpoa_graph.c:600:78: style:inconclusive: Boolean expression 'abpt->max_n_cons>1' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
abPOA-1.5.3/src/abpoa_graph.c:9:1: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
abPOA-1.5.3/src/abpoa_graph.c:9:1: note: Assuming allocation function fails
abPOA-1.5.3/src/abpoa_graph.c:9:1: note: Assignment 'q=(struct kdq_int_t*)calloc(1,sizeof(struct kdq_int_t))', assigned value is 0
abPOA-1.5.3/src/abpoa_graph.c:9:1: note: Null pointer dereference
abPOA-1.5.3/src/abpoa_graph.c:110:38: style:inconclusive: Function 'abpoa_free_graph' argument 1 names different: declaration 'graph' definition 'abg'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa_graph.h:25:38: note: Function 'abpoa_free_graph' argument 1 names different: declaration 'graph' definition 'abg'.
abPOA-1.5.3/src/abpoa_graph.c:110:38: note: Function 'abpoa_free_graph' argument 1 names different: declaration 'graph' definition 'abg'.
abPOA-1.5.3/src/abpoa_graph.c:573:64: style:inconclusive: Function 'abpoa_subgraph_nodes' argument 3 names different: declaration 'inc_beg' definition 'exc_beg0'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:167:64: note: Function 'abpoa_subgraph_nodes' argument 3 names different: declaration 'inc_beg' definition 'exc_beg0'.
abPOA-1.5.3/src/abpoa_graph.c:573:64: note: Function 'abpoa_subgraph_nodes' argument 3 names different: declaration 'inc_beg' definition 'exc_beg0'.
abPOA-1.5.3/src/abpoa_graph.c:573:78: style:inconclusive: Function 'abpoa_subgraph_nodes' argument 4 names different: declaration 'inc_end' definition 'exc_end0'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:167:77: note: Function 'abpoa_subgraph_nodes' argument 4 names different: declaration 'inc_end' definition 'exc_end0'.
abPOA-1.5.3/src/abpoa_graph.c:573:78: note: Function 'abpoa_subgraph_nodes' argument 4 names different: declaration 'inc_end' definition 'exc_end0'.
abPOA-1.5.3/src/abpoa_graph.c:596:110: style:inconclusive: Function 'abpoa_add_subgraph_alignment' argument 5 names different: declaration 'query' definition 'seq'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:192:110: note: Function 'abpoa_add_subgraph_alignment' argument 5 names different: declaration 'query' definition 'seq'.
abPOA-1.5.3/src/abpoa_graph.c:596:110: note: Function 'abpoa_add_subgraph_alignment' argument 5 names different: declaration 'query' definition 'seq'.
abPOA-1.5.3/src/abpoa_graph.c:596:120: style:inconclusive: Function 'abpoa_add_subgraph_alignment' argument 6 names different: declaration 'weight' definition '_weight'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:192:122: note: Function 'abpoa_add_subgraph_alignment' argument 6 names different: declaration 'weight' definition '_weight'.
abPOA-1.5.3/src/abpoa_graph.c:596:120: note: Function 'abpoa_add_subgraph_alignment' argument 6 names different: declaration 'weight' definition '_weight'.
abPOA-1.5.3/src/abpoa_graph.c:596:133: style:inconclusive: Function 'abpoa_add_subgraph_alignment' argument 7 names different: declaration 'qlen' definition 'seq_l'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:192:134: note: Function 'abpoa_add_subgraph_alignment' argument 7 names different: declaration 'qlen' definition 'seq_l'.
abPOA-1.5.3/src/abpoa_graph.c:596:133: note: Function 'abpoa_add_subgraph_alignment' argument 7 names different: declaration 'qlen' definition 'seq_l'.
abPOA-1.5.3/src/abpoa_graph.c:674:73: style:inconclusive: Function 'abpoa_add_graph_alignment' argument 3 names different: declaration 'query' definition 'seq'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:191:73: note: Function 'abpoa_add_graph_alignment' argument 3 names different: declaration 'query' definition 'seq'.
abPOA-1.5.3/src/abpoa_graph.c:674:73: note: Function 'abpoa_add_graph_alignment' argument 3 names different: declaration 'query' definition 'seq'.
abPOA-1.5.3/src/abpoa_graph.c:674:95: style:inconclusive: Function 'abpoa_add_graph_alignment' argument 5 names different: declaration 'qlen' definition 'seq_l'. [funcArgNamesDifferent]
abPOA-1.5.3/src/abpoa.h:191:97: note: Function 'abpoa_add_graph_alignment' argument 5 names different: declaration 'qlen' definition 'seq_l'.
abPOA-1.5.3/src/abpoa_graph.c:674:95: note: Function 'abpoa_add_graph_alignment' argument 5 names different: declaration 'qlen' definition 'seq_l'.
abPOA-1.5.3/src/abpoa_plot.c:48:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_graph.c:187:10: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_graph.c:234:10: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_graph.c:279:63: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_graph.c:321:10: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_graph.c:486:60: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_graph.c:486:70: style: Parameter 'weight' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_graph.c:596:61: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_graph.c:598:47: style: Variable 'abpoa_cigar' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_graph.c:681:45: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_plot.c:52:12: warning: If memory allocation fails, then there is a possible null pointer dereference: dot_fn [nullPointerOutOfMemory]
abPOA-1.5.3/src/abpoa_plot.c:51:33: note: Assuming allocation function fails
abPOA-1.5.3/src/abpoa_plot.c:51:20: note: Assignment 'dot_fn=(char*)malloc(strlen(abpt->out_pog)+10)', assigned value is 0
abPOA-1.5.3/src/abpoa_plot.c:52:12: note: Null pointer dereference
abPOA-1.5.3/src/abpoa_plot.c:53:16: warning: If memory allocation fails, then there is a possible null pointer dereference: dot_fn [nullPointerOutOfMemory]
abPOA-1.5.3/src/abpoa_plot.c:51:33: note: Assuming allocation function fails
abPOA-1.5.3/src/abpoa_plot.c:51:20: note: Assignment 'dot_fn=(char*)malloc(strlen(abpt->out_pog)+10)', assigned value is 0
abPOA-1.5.3/src/abpoa_plot.c:53:16: note: Null pointer dereference
abPOA-1.5.3/src/abpoa_plot.c:41:10: style: Variable 'node_color' can be declared as const array [constVariable]
abPOA-1.5.3/src/abpoa_plot.c:44:10: style: Variable 'rankdir' can be declared as const array [constVariable]
abPOA-1.5.3/src/abpoa_plot.c:44:29: style: Variable 'node_style' can be declared as const array [constVariable]
abPOA-1.5.3/src/abpoa_plot.c:44:54: style: Variable 'node_fixedsize' can be declared as const array [constVariable]
abPOA-1.5.3/src/abpoa_plot.c:44:81: style: Variable 'node_shape' can be declared as const array [constVariable]
abPOA-1.5.3/src/abpoa_plot.c:115:11: style: Variable 'type' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:49:1: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
abPOA-1.5.3/src/abpoa_output.c:49:1: note: Assuming allocation function fails
abPOA-1.5.3/src/abpoa_output.c:49:1: note: Assignment 'q=(struct kdq_int_t*)calloc(1,sizeof(struct kdq_int_t))', assigned value is 0
abPOA-1.5.3/src/abpoa_output.c:49:1: note: Null pointer dereference
abPOA-1.5.3/src/abpoa_seed.c:25:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable x [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:25:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable e [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:28:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable y [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:28:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable e [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:31:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable e [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:234:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:461:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:521:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:616:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:684:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:691:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seed.c:707:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_output.c:52:42: style: Parameter 'read_ids' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:70:53: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:73:18: style: Variable 'abs' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:73:47: style: Variable 'abc' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:129:18: style: Variable 'abs' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:171:18: style: Variable 'abs' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:178:40: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:437:64: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:437:100: style: Parameter 'out_degree' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:438:10: style: Variable 'id' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:507:59: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:543:59: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:546:19: style: Variable 'abc' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_output.c:681:113: style: Parameter 'clu_poss' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:847:41: style: Parameter 'het_poss' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_output.c:941:15: warning: Uninitialized variable: m_clu [uninitvar]
abPOA-1.5.3/src/abpoa_output.c:932:19: note: Assuming condition is true
abPOA-1.5.3/src/abpoa_output.c:941:15: note: Uninitialized variable: m_clu
abPOA-1.5.3/src/kalloc.c:34:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.h:141:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.h:163:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.h:179:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.h:194:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.h:216:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.h:237:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.h:259:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:103:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:126:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:142:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:309:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:347:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:403:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:483:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:561:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:644:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kalloc.c:49:23: style:inconclusive: Function 'km_destroy' argument 1 names different: declaration 'km' definition '_km'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:21:23: note: Function 'km_destroy' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:49:23: note: Function 'km_destroy' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:79:18: style:inconclusive: Function 'kfree' argument 1 names different: declaration 'km' definition '_km'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:17:18: note: Function 'kfree' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:79:18: note: Function 'kfree' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:79:29: style:inconclusive: Function 'kfree' argument 2 names different: declaration 'ptr' definition 'ap'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:17:28: note: Function 'kfree' argument 2 names different: declaration 'ptr' definition 'ap'.
abPOA-1.5.3/src/kalloc.c:79:29: note: Function 'kfree' argument 2 names different: declaration 'ptr' definition 'ap'.
abPOA-1.5.3/src/kalloc.c:127:21: style:inconclusive: Function 'kmalloc' argument 1 names different: declaration 'km' definition '_km'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:14:21: note: Function 'kmalloc' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:127:21: note: Function 'kmalloc' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:127:33: style:inconclusive: Function 'kmalloc' argument 2 names different: declaration 'size' definition 'n_bytes'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:14:32: note: Function 'kmalloc' argument 2 names different: declaration 'size' definition 'n_bytes'.
abPOA-1.5.3/src/kalloc.c:127:33: note: Function 'kmalloc' argument 2 names different: declaration 'size' definition 'n_bytes'.
abPOA-1.5.3/src/kalloc.c:156:21: style:inconclusive: Function 'kcalloc' argument 1 names different: declaration 'km' definition '_km'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:16:21: note: Function 'kcalloc' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:156:21: note: Function 'kcalloc' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:167:22: style:inconclusive: Function 'krealloc' argument 1 names different: declaration 'km' definition '_km'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:15:22: note: Function 'krealloc' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:167:22: note: Function 'krealloc' argument 1 names different: declaration 'km' definition '_km'.
abPOA-1.5.3/src/kalloc.c:167:33: style:inconclusive: Function 'krealloc' argument 2 names different: declaration 'ptr' definition 'ap'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:15:32: note: Function 'krealloc' argument 2 names different: declaration 'ptr' definition 'ap'.
abPOA-1.5.3/src/kalloc.c:167:33: note: Function 'krealloc' argument 2 names different: declaration 'ptr' definition 'ap'.
abPOA-1.5.3/src/kalloc.c:167:44: style:inconclusive: Function 'krealloc' argument 3 names different: declaration 'size' definition 'n_bytes'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kalloc.h:15:44: note: Function 'krealloc' argument 3 names different: declaration 'size' definition 'n_bytes'.
abPOA-1.5.3/src/kalloc.c:167:44: note: Function 'krealloc' argument 3 names different: declaration 'size' definition 'n_bytes'.
abPOA-1.5.3/src/kalloc.c:170:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/kstring.c:119:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/kstring.c:148:3: warning: If memory allocation fails, then there is a possible null pointer dereference: suff [nullPointerOutOfMemory]
abPOA-1.5.3/src/kstring.c:145:21: note: Assuming allocation function fails
abPOA-1.5.3/src/kstring.c:145:9: note: Assignment 'suff=(int*)calloc(m,sizeof(int))', assigned value is 0
abPOA-1.5.3/src/kstring.c:148:3: note: Null pointer dereference
abPOA-1.5.3/src/kstring.c:151:17: warning: If memory allocation fails, then there is a possible null pointer dereference: suff [nullPointerOutOfMemory]
abPOA-1.5.3/src/kstring.c:145:21: note: Assuming allocation function fails
abPOA-1.5.3/src/kstring.c:145:9: note: Assignment 'suff=(int*)calloc(m,sizeof(int))', assigned value is 0
abPOA-1.5.3/src/kstring.c:151:17: note: Null pointer dereference
abPOA-1.5.3/src/kstring.c:140:27: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
abPOA-1.5.3/src/kstring.c:139:21: note: Assuming allocation function fails
abPOA-1.5.3/src/kstring.c:139:9: note: Assignment 'prep=(int*)calloc(m+256,sizeof(int))', assigned value is 0
abPOA-1.5.3/src/kstring.c:140:27: note: Null pointer addition
abPOA-1.5.3/src/kstring.c:37:44: style:inconclusive: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'. [funcArgNamesDifferent]
abPOA-1.5.3/src/kstring.h:83:45: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
abPOA-1.5.3/src/kstring.c:37:44: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
abPOA-1.5.3/src/kstring.c:178:31: style: Variable 'bmBc' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/kstring.h:110:39: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/kstring.h:115:40: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:193:61: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
abPOA-1.5.3/src/abpoa_seed.c:359:21: style: Condition 'xi>xj' is always true [knownConditionTrueFalse]
abPOA-1.5.3/src/abpoa_seed.c:339:16: note: Assuming that condition 'xi==xj' is not redundant
abPOA-1.5.3/src/abpoa_seed.c:359:21: note: Condition 'xi>xj' is always true
abPOA-1.5.3/src/abpoa_seed.c:461:13: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
abPOA-1.5.3/src/abpoa_seed.c:461:13: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
abPOA-1.5.3/src/abpoa_seed.c:684:13: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
abPOA-1.5.3/src/abpoa_seed.c:684:13: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
abPOA-1.5.3/src/abpoa_seed.c:734:56: portability: %ld in format string (no. 3) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
abPOA-1.5.3/src/abpoa_seed.c:231:42: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:366:103: style: Parameter 'pre_id' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:366:116: style: Parameter 'score' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:487:89: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:580:32: style: Parameter 'lis' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:660:25: style: Variable 'rank' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_seed.c:690:53: style: Parameter 'seq_lens' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:690:88: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seed.c:86:21: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
abPOA-1.5.3/src/utils.c:61:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:71:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:80:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:95:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:106:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:115:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:121:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:129:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:138:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:151:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:162:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:172:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:179:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:196:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:208:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:221:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:230:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:241:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:252:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:259:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:270:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:297:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:306:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:342:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RUSAGE_SELF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:350:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RUSAGE_SELF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:365:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RUSAGE_SELF [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:396:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/utils.c:377:11: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
abPOA-1.5.3/src/utils.c:389:12: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
abPOA-1.5.3/src/utils.c:70:6: error: Return value of allocation function 'freopen' is not stored. [leakReturnValNotUsed]
abPOA-1.5.3/src/utils.c:51:1: warning: If memory allocation fails, then there is a possible null pointer dereference: ks [nullPointerOutOfMemory]
abPOA-1.5.3/src/utils.c:51:1: note: Assuming allocation function fails
abPOA-1.5.3/src/utils.c:51:1: note: Assignment 'ks=(struct kstream_t*)calloc(1,sizeof(struct kstream_t))', assigned value is 0
abPOA-1.5.3/src/utils.c:51:1: note: Null pointer dereference
abPOA-1.5.3/src/utils.c:51:1: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
abPOA-1.5.3/src/utils.c:51:1: note: Assuming allocation function fails
abPOA-1.5.3/src/utils.c:51:1: note: Assignment 's=(struct kseq_t*)calloc(1,sizeof(struct kseq_t))', assigned value is 0
abPOA-1.5.3/src/utils.c:51:1: note: Null pointer dereference
abPOA-1.5.3/src/utils.c:385:16: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_seq.c:236:112: style: Redundant condition: The condition 'type == 'I'' is redundant since 'type != 'f'' is sufficient. [redundantCondition]
abPOA-1.5.3/src/abpoa_seq.c:598:17: style: Condition 'fn' is always true [knownConditionTrueFalse]
abPOA-1.5.3/sub_example.c:114:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/abpoa_seq.c:285:18: warning: Either the condition 'aux' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
abPOA-1.5.3/src/abpoa_seq.c:325:9: note: Assuming that condition 'aux' is not redundant
abPOA-1.5.3/src/abpoa_seq.c:308:31: note: Calling function 'gfa_aux_get', 2nd argument 'aux' value is 0
abPOA-1.5.3/src/abpoa_seq.c:285:18: note: Null pointer addition
abPOA-1.5.3/src/abpoa_seq.c:479:15: style: Local variable 'deli_s' shadows outer variable [shadowVariable]
abPOA-1.5.3/src/abpoa_seq.c:456:11: note: Shadowed declaration
abPOA-1.5.3/src/abpoa_seq.c:479:15: note: Shadow variable
abPOA-1.5.3/src/abpoa_seq.c:479:24: style: Local variable 'info_s' shadows outer variable [shadowVariable]
abPOA-1.5.3/src/abpoa_seq.c:456:20: note: Shadowed declaration
abPOA-1.5.3/src/abpoa_seq.c:479:24: note: Shadow variable
abPOA-1.5.3/src/abpoa_seq.c:123:44: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seq.c:294:38: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/abpoa_seq.c:374:29: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_seq.c:459:16: style: Variable 'seg_seq' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_seq.c:459:26: style: Variable 'seg_name' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/abpoa_seq.c:323:11: style: Variable 'l_aux' is assigned a value that is never used. [unreadVariable]
abPOA-1.5.3/sub_example.c:100:9: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:97:33: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:97:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:100:9: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:101:9: warning: If memory allocation fails, then there is a possible null pointer dereference: bseqs [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:98:40: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:98:23: note: Assignment 'bseqs=(uint8_t**)malloc(sizeof(uint8_t*)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:101:9: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:101:55: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:97:33: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:97:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:101:55: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:102:25: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:97:33: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:97:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:102:25: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:103:13: warning: If memory allocation fails, then there is a possible null pointer dereference: bseqs [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:98:40: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:98:23: note: Assignment 'bseqs=(uint8_t**)malloc(sizeof(uint8_t*)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:103:13: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:115:70: warning: If memory allocation fails, then there is a possible null pointer dereference: bseqs [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:98:40: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:98:23: note: Assignment 'bseqs=(uint8_t**)malloc(sizeof(uint8_t*)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:115:70: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:115:80: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:97:33: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:97:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:115:80: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:116:66: warning: If memory allocation fails, then there is a possible null pointer dereference: bseqs [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:98:40: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:98:23: note: Assignment 'bseqs=(uint8_t**)malloc(sizeof(uint8_t*)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:116:66: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:116:82: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_lens [nullPointerOutOfMemory]
abPOA-1.5.3/sub_example.c:97:33: note: Assuming allocation function fails
abPOA-1.5.3/sub_example.c:97:21: note: Assignment 'seq_lens=(int*)malloc(sizeof(int)*n_seqs)', assigned value is 0
abPOA-1.5.3/sub_example.c:116:82: note: Null pointer dereference
abPOA-1.5.3/sub_example.c:36:10: style: Variable 'seqs' can be declared as const array [constVariable]
abPOA-1.5.3/sub_example.c:51:9: style: Variable 'beg_end_id' can be declared as const array [constVariable]
abPOA-1.5.3/src/simd_abpoa_align.c:41:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_abpoa_align.c:1226:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_abpoa_align.c:1350:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_abpoa_align.c:1597:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_abpoa_align.c:1664:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_abpoa_align.c:1719:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
abPOA-1.5.3/src/simd_abpoa_align.c:1499:17: style: Condition 'hit==0' is always true [knownConditionTrueFalse]
abPOA-1.5.3/src/simd_abpoa_align.c:1482:66: note: Assignment 'hit=0', assigned value is 0
abPOA-1.5.3/src/simd_abpoa_align.c:1499:17: note: Condition 'hit==0' is always true
abPOA-1.5.3/src/simd_abpoa_align.c:1626:13: style: Same expression used in consecutive assignments of 'best_score' and 'inf_min'. [duplicateAssignExpression]
abPOA-1.5.3/src/simd_abpoa_align.c:1626:38: note: Same expression used in consecutive assignments of 'best_score' and 'inf_min'.
abPOA-1.5.3/src/simd_abpoa_align.c:1626:13: note: Same expression used in consecutive assignments of 'best_score' and 'inf_min'.
abPOA-1.5.3/src/simd_abpoa_align.c:38:33: style: Parameter 'pre_index' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1210:69: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1243:35: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1243:50: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1248:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1260:38: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1260:75: style: Parameter 'index_map' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1295:14: style: Variable '_dp_h' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1295:39: style: Variable '_qi' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1317:90: style: Parameter 'index_map' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1317:147: style: Parameter 'dp_end' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1325:18: style: Variable '_dp_h' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1336:39: style: Parameter 'pre_n' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1336:120: style: Parameter 'abpt' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1467:64: style: Parameter 'pre_n' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1467:76: style: Parameter 'dp_beg' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1467:89: style: Parameter 'dp_end' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1468:37: style: Parameter 'mat' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1470:76: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:27: style: Variable '_dp_h' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:40: style: Variable '_dp_e1' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:49: style: Variable '_dp_e2' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:58: style: Variable '_pre_dp_h' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:70: style: Variable '_pre_dp_e1' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:83: style: Variable '_pre_dp_e2' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:96: style: Variable '_dp_f1' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1473:105: style: Variable '_dp_f2' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1481:14: style: Variable 'pre_index_i' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1703:56: style: Variable '_dp_h' can be declared as pointer to const [constVariablePointer]
abPOA-1.5.3/src/simd_abpoa_align.c:1717:119: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
diff:
2.17.0 abPOA-1.5.3/src/kstring.c:140:27: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     abPOA-1.5.3/src/kstring.c:139:21: note: Assuming allocation function fails
     abPOA-1.5.3/src/kstring.c:139:9: note: Assignment 'prep=(int*)calloc(m+256,sizeof(int))', assigned value is 0
     abPOA-1.5.3/src/kstring.c:140:27: note: Null pointer addition
head abPOA-1.5.3/src/kstring.c:140:27: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     abPOA-1.5.3/src/kstring.c:139:21: note: Assuming allocation function fails
     abPOA-1.5.3/src/kstring.c:139:9: note: Assignment 'prep=(int*)calloc(m+256,sizeof(int))', assigned value is 0
     abPOA-1.5.3/src/kstring.c:140:27: note: Null pointer addition


DONE