2025-05-07 15:17
ftp://ftp.de.debian.org/debian/pool/main/r/r-bioc-rsubread/r-bioc-rsubread_2.20.0.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: 3726ace (2025-05-07 13:02:19 +0200)
count: 2560 2524
elapsed-time: 34.0 36.3
head-timing-info:

old-timing-info:

head results:
Rsubread/src/HelperFunctions.c:1078:44: debug: Function::addArguments found argument 'gene_name' with varid 0. [varid0]
Rsubread/src/LRMbase-index.c:92:3: error: Resource leak: fp [resourceLeak]
Rsubread/src/LRMbase-index.c:97:3: error: Resource leak: fp [resourceLeak]
Rsubread/src/LRMbase-index.c:109:3: error: Resource leak: fp [resourceLeak]
Rsubread/src/LRMbase-index.c:116:3: error: Resource leak: fp [resourceLeak]
Rsubread/src/LRMbase-index.c:89:47: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/LRMbase-index.c:87:19: note: Assuming allocation function fails
Rsubread/src/LRMbase-index.c:87:19: note: Assignment 'fp=fopen(filename,"rb")', assigned value is 0
Rsubread/src/LRMbase-index.c:89:47: note: Null pointer dereference
Rsubread/src/LRMbase-index.c:94:42: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/LRMbase-index.c:87:19: note: Assuming allocation function fails
Rsubread/src/LRMbase-index.c:87:19: note: Assignment 'fp=fopen(filename,"rb")', assigned value is 0
Rsubread/src/LRMbase-index.c:90:16: note: Assuming condition is false
Rsubread/src/LRMbase-index.c:94:42: note: Null pointer dereference
Rsubread/src/LRMbase-index.c:144:129: style:inconclusive: Function 'LRMvalidate_mapping' argument 6 names different: declaration 'rev' definition 'neg'. [funcArgNamesDifferent]
Rsubread/src/LRMbase-index.h:37:129: note: Function 'LRMvalidate_mapping' argument 6 names different: declaration 'rev' definition 'neg'.
Rsubread/src/LRMbase-index.c:144:129: note: Function 'LRMvalidate_mapping' argument 6 names different: declaration 'rev' definition 'neg'.
Rsubread/src/LRMbase-index.c:144:140: style:inconclusive: Function 'LRMvalidate_mapping' argument 7 names different: declaration 'mapped_length' definition 'maplen'. [funcArgNamesDifferent]
Rsubread/src/LRMbase-index.h:37:140: note: Function 'LRMvalidate_mapping' argument 7 names different: declaration 'mapped_length' definition 'maplen'.
Rsubread/src/LRMbase-index.c:144:140: note: Function 'LRMvalidate_mapping' argument 7 names different: declaration 'mapped_length' definition 'maplen'.
Rsubread/src/LRMbase-index.c:33:81: style: Parameter 'index' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMbase-index.c:211:26: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMbase-index.c:146:55: style: Variable 'all_mismatched' is assigned a value that is never used. [unreadVariable]
Rsubread/src/LRMbase-index.c:183:20: style: Variable 'all_mismatched' is assigned a value that is never used. [unreadVariable]
Rsubread/src/LRMfile-io.c:103:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/LRMfile-io.c:121:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/HelperFunctions.c:1885:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
Rsubread/src/LRMfile-io.c:331:2: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/LRMfile-io.c:337:2: warning: Return value of function deflate() is not used. [ignoredReturnValue]
Rsubread/src/LRMfile-io.c:71:29: style:inconclusive: Function 'LRMreverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. [funcArgNamesDifferent]
Rsubread/src/LRMfile-io.h:29:29: note: Function 'LRMreverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'.
Rsubread/src/LRMfile-io.c:71:29: note: Function 'LRMreverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'.
Rsubread/src/LRMfile-io.c:71:41: style:inconclusive: Function 'LRMreverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent]
Rsubread/src/LRMfile-io.h:29:45: note: Function 'LRMreverse_read' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/LRMfile-io.c:71:41: note: Function 'LRMreverse_read' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/LRMfile-io.c:183:32: style:inconclusive: Function 'LRMreverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. [funcArgNamesDifferent]
Rsubread/src/LRMfile-io.h:30:32: note: Function 'LRMreverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'.
Rsubread/src/LRMfile-io.c:183:32: note: Function 'LRMreverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'.
Rsubread/src/LRMfile-io.c:183:44: style:inconclusive: Function 'LRMreverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent]
Rsubread/src/LRMfile-io.h:30:50: note: Function 'LRMreverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/LRMfile-io.c:183:44: note: Function 'LRMreverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/LRMfile-io.c:633:103: style:inconclusive: Function 'LRMlocate_chro_length' argument 4 names different: declaration 'chro_len' definition 'end_pos'. [funcArgNamesDifferent]
Rsubread/src/LRMfile-io.h:35:103: note: Function 'LRMlocate_chro_length' argument 4 names different: declaration 'chro_len' definition 'end_pos'.
Rsubread/src/LRMfile-io.c:633:103: note: Function 'LRMlocate_chro_length' argument 4 names different: declaration 'chro_len' definition 'end_pos'.
Rsubread/src/LRMfile-io.c:506:7: style: Local variable 'new_need' shadows outer variable [shadowVariable]
Rsubread/src/LRMfile-io.c:496:6: note: Shadowed declaration
Rsubread/src/LRMfile-io.c:506:7: note: Shadow variable
Rsubread/src/LRMfile-io.c:22:25: style: Parameter 'key' can be declared as const array [constParameter]
Rsubread/src/LRMfile-io.c:203:56: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMfile-io.c:203:89: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMfile-io.c:250:64: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMfile-io.c:250:77: style: Parameter 'qual' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMfile-io.c:272:199: style: Parameter 'chro_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMfile-io.c:311:31: style: Parameter 'dat' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMfile-io.c:370:17: style: Variable 's' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMfile-io.c:504:10: style: Variable 'chro_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMhashtable.c:786:70: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
Rsubread/src/LRMhashtable.c:28:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/LRMhashtable.c:27:26: note: Assuming allocation function fails
Rsubread/src/LRMhashtable.c:27:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/LRMhashtable.c:28:9: note: Null pointer dereference
Rsubread/src/LRMhashtable.c:29:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/LRMhashtable.c:27:26: note: Assuming allocation function fails
Rsubread/src/LRMhashtable.c:27:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/LRMhashtable.c:29:2: note: Null pointer dereference
Rsubread/src/LRMhashtable.c:30:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/LRMhashtable.c:27:26: note: Assuming allocation function fails
Rsubread/src/LRMhashtable.c:27:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/LRMhashtable.c:30:2: note: Null pointer dereference
Rsubread/src/LRMhashtable.c:740:40: style:inconclusive: Function 'LRMisProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. [funcArgNamesDifferent]
Rsubread/src/LRMhashtable.c:22:40: note: Function 'LRMisProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'.
Rsubread/src/LRMhashtable.c:740:40: note: Function 'LRMisProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'.
Rsubread/src/LRMhashtable.c:752:58: style: Parameter 'hashTable' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMseek-zlib.c:295:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/LRMseek-zlib.c:186:68: warning: Assert statement calls a function which may have desired side effects: 'feof'. [assertWithSideEffect]
Rsubread/src/LRMseek-zlib.c:15:32: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMseek-zlib.c:138:40: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMseek-zlib.c:194:31: style: Variable 'this_chunk_size' is assigned a value that is never used. [unreadVariable]
Rsubread/src/LRMseek-zlib.c:274:20: style: Variable 'this_chunk_size' is assigned a value that is never used. [unreadVariable]
Rsubread/src/LRMseek-zlib.c:278:50: style: Variable 'this_chunk_size' is assigned a value that is never used. [unreadVariable]
Rsubread/src/LRMsorted-hashtable.c:209:11: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
Rsubread/src/LRMsorted-hashtable.c:562:11: style: Condition '0&&LRMFIXLENstrcmp("@39076b1f-df29-4487-be51-4c30bf6c1cc4_Basecall_Alignment_template",iteration_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/LRMsorted-hashtable.c:271:4: error: Resource leak: fp [resourceLeak]
Rsubread/src/LRMsorted-hashtable.c:328:3: error: Resource leak: fp [resourceLeak]
Rsubread/src/LRMsorted-hashtable.c:55:64: style:inconclusive: Function 'LRMgehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent]
Rsubread/src/LRMsorted-hashtable.h:31:64: note: Function 'LRMgehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/LRMsorted-hashtable.c:55:64: note: Function 'LRMgehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/LRMsorted-hashtable.c:443:176: style:inconclusive: Function 'LRMgehash_go_QQ' argument 5 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent]
Rsubread/src/LRMsorted-hashtable.h:44:176: note: Function 'LRMgehash_go_QQ' argument 5 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/LRMsorted-hashtable.c:443:176: note: Function 'LRMgehash_go_QQ' argument 5 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/LRMsorted-hashtable.c:37:63: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMsorted-hashtable.c:64:9: style: Variable 'current_keys' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMsorted-hashtable.c:110:25: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMsorted-hashtable.c:202:68: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMsorted-hashtable.c:448:9: style: Variable 'current_keys' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMsorted-hashtable.c:427:24: error: Shifting signed 32-bit value by 31 bits is undefined behaviour [shiftTooManyBitsSigned]
Rsubread/src/LRMsorted-hashtable.c:426:14: note: Assuming that condition 'xx<32' is not redundant
Rsubread/src/LRMsorted-hashtable.c:427:24: note: Shift
Rsubread/src/LRMsorted-hashtable.c:446:8: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
Rsubread/src/LRMsorted-hashtable.c:515:9: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
Rsubread/src/LRMsorted-hashtable.c:542:23: style: Variable 'base_to_change' is assigned a value that is never used. [unreadVariable]
Rsubread/src/R_wrapper.c:559:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar]
Rsubread/src/R_wrapper.c:112:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:113:38: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:140:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:141:38: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:158:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:159:40: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:180:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:181:38: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:206:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:207:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:231:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:232:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:252:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:253:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:277:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:279:22: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:307:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:308:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:332:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:333:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:353:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:354:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:387:28: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:426:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:427:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:452:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:453:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:475:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:476:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:495:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:497:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:516:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:517:36: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/R_wrapper.c:59:5: warning: If memory allocation fails, then there is a possible null pointer dereference: opts [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:58:49: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:58:49: note: Assignment 'opts=malloc(sizeof(struct R_child_thread_run_opt))', assigned value is 0
Rsubread/src/R_wrapper.c:59:5: note: Null pointer dereference
Rsubread/src/R_wrapper.c:60:5: warning: If memory allocation fails, then there is a possible null pointer dereference: opts [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:58:49: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:58:49: note: Assignment 'opts=malloc(sizeof(struct R_child_thread_run_opt))', assigned value is 0
Rsubread/src/R_wrapper.c:60:5: note: Null pointer dereference
Rsubread/src/R_wrapper.c:61:5: warning: If memory allocation fails, then there is a possible null pointer dereference: opts [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:58:49: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:58:49: note: Assignment 'opts=malloc(sizeof(struct R_child_thread_run_opt))', assigned value is 0
Rsubread/src/R_wrapper.c:61:5: note: Null pointer dereference
Rsubread/src/R_wrapper.c:110:21: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:110:21: note: Null pointer dereference
Rsubread/src/R_wrapper.c:111:9: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:111:9: note: Null pointer dereference
Rsubread/src/R_wrapper.c:112:9: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:112:9: note: Null pointer dereference
Rsubread/src/R_wrapper.c:113:28: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:113:28: note: Null pointer dereference
Rsubread/src/R_wrapper.c:117:8: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:117:8: note: Null pointer dereference
Rsubread/src/R_wrapper.c:119:18: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:119:18: note: Null pointer dereference
Rsubread/src/R_wrapper.c:120:28: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:120:28: note: Null pointer dereference
Rsubread/src/R_wrapper.c:121:33: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:121:33: note: Null pointer dereference
Rsubread/src/R_wrapper.c:122:31: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:108:35: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:108:19: note: Assignment 'c_argv=(char**)calloc(n+1+4,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:122:31: note: Null pointer dereference
Rsubread/src/R_wrapper.c:156:19: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:155:27: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:155:11: note: Assignment 'c_argv=(char**)calloc(n+1,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:156:19: note: Null pointer dereference
Rsubread/src/R_wrapper.c:157:9: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:155:27: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:155:11: note: Assignment 'c_argv=(char**)calloc(n+1,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:157:9: note: Null pointer dereference
Rsubread/src/R_wrapper.c:158:2: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:155:27: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:155:11: note: Assignment 'c_argv=(char**)calloc(n+1,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:158:2: note: Null pointer dereference
Rsubread/src/R_wrapper.c:277:2: warning: If memory allocation fails, then there is a possible null pointer dereference: c_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:276:27: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:276:11: note: Assignment 'c_argv=(char**)calloc(n,sizeof(char*))', assigned value is 0
Rsubread/src/R_wrapper.c:277:2: note: Null pointer dereference
Rsubread/src/R_wrapper.c:378:10: warning: If memory allocation fails, then there is a possible null pointer dereference: r_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:377:26: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:377:12: note: Assignment 'r_argv=(char*)calloc(1+arg_len,sizeof(char))', assigned value is 0
Rsubread/src/R_wrapper.c:378:10: note: Null pointer dereference
Rsubread/src/R_wrapper.c:383:13: warning: If memory allocation fails, then there is a possible null pointer dereference: r_argv [nullPointerOutOfMemory]
Rsubread/src/R_wrapper.c:377:26: note: Assuming allocation function fails
Rsubread/src/R_wrapper.c:377:12: note: Assignment 'r_argv=(char*)calloc(1+arg_len,sizeof(char))', assigned value is 0
Rsubread/src/R_wrapper.c:383:13: note: Null pointer dereference
Rsubread/src/R_wrapper.c:100:39: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_try_cell_barcode_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:552:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:100:39: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:130:31: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_txUnique_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:532:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:130:31: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:148:25: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_cellCounts' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:533:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:148:25: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:168:23: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_mergeVCF' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:534:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:168:23: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:192:30: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_sublong_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:535:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:192:30: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:222:29: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_repair_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:536:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:222:29: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:241:33: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_buildindex_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:537:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:241:33: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:263:28: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_align_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:538:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:263:28: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:293:31: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_junction_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:539:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:293:31: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:322:30: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_sam2bed_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:540:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:322:30: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:343:33: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_propmapped_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:541:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:343:33: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:411:33: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_SNPcalling_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:543:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:411:33: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:441:37: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_removeDupReads_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:544:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:441:37: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:464:36: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_qualityScores_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:545:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:464:36: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:486:43: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_generate_random_RNAseq_reads' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:546:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:486:43: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/R_wrapper.c:507:33: style: Parameter 'nargs' can be declared as pointer to const. However it seems that 'R_flattenGTF_wrapper' is a callback function, if 'nargs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/R_wrapper.c:547:49: note: You might need to cast the function pointer here
Rsubread/src/R_wrapper.c:507:33: note: Parameter 'nargs' can be declared as pointer to const
Rsubread/src/LRMchro-event.c:490:42: warning: Either the condition 'row_i>=0' is redundant or the array 'best_offset_history[2147483648]' is accessed at index -1, which is out of bounds. [negativeIndex]
Rsubread/src/LRMchro-event.c:489:14: note: Assuming that condition 'row_i>=0' is not redundant
Rsubread/src/LRMchro-event.c:490:42: note: Negative array index
Rsubread/src/LRMchro-event.c:179:9: style: Condition '1||te->small_side==457511654' is always true [knownConditionTrueFalse]
Rsubread/src/LRMchro-event.c:622:8: style: Condition '0&&!search_to_3end' is always false [knownConditionTrueFalse]
Rsubread/src/LRMchro-event.c:674:10: style: Condition '0&&!search_to_3end' is always false [knownConditionTrueFalse]
Rsubread/src/LRMchro-event.c:688:8: style: Condition '0&&!search_to_3end' is always false [knownConditionTrueFalse]
Rsubread/src/LRMchro-event.c:114:5: error: Common realloc mistake: 'entries_list' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/LRMchro-event.c:143:5: error: Common realloc mistake: 'new_space' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/LRMchro-event.c:65:26: warning: If memory allocation fails, then there is a possible null pointer dereference: merged_records [nullPointerOutOfMemory]
Rsubread/src/LRMchro-event.c:57:31: note: Assuming allocation function fails
Rsubread/src/LRMchro-event.c:57:31: note: Assignment 'merged_records=malloc(sizeof(int)*(items+items2))', assigned value is 0
Rsubread/src/LRMchro-event.c:65:26: note: Null pointer dereference
Rsubread/src/LRMchro-event.c:95:5: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck]
Rsubread/src/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant
Rsubread/src/LRMchro-event.c:95:5: note: Null pointer dereference
Rsubread/src/LRMchro-event.c:96:5: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck]
Rsubread/src/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant
Rsubread/src/LRMchro-event.c:96:5: note: Null pointer dereference
Rsubread/src/LRMchro-event.c:100:21: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck]
Rsubread/src/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant
Rsubread/src/LRMchro-event.c:100:21: note: Null pointer dereference
Rsubread/src/LRMchro-event.c:104:13: warning: Either the condition '!entries_list' is redundant or there is possible null pointer dereference: entries_list. [nullPointerRedundantCheck]
Rsubread/src/LRMchro-event.c:91:8: note: Assuming that condition '!entries_list' is not redundant
Rsubread/src/LRMchro-event.c:104:13: note: Null pointer dereference
Rsubread/src/LRMchro-event.c:164:3: warning: If memory allocation fails, then there is a possible null pointer dereference: order_index [nullPointerOutOfMemory]
Rsubread/src/LRMchro-event.c:161:28: note: Assuming allocation function fails
Rsubread/src/LRMchro-event.c:161:28: note: Assignment 'order_index=malloc(context->event_number*sizeof(int))', assigned value is 0
Rsubread/src/LRMchro-event.c:164:3: note: Null pointer dereference
Rsubread/src/LRMchro-event.c:637:108: style: Same expression 'read_i>0' found multiple times in chain of '&&' operators. [duplicateExpression]
Rsubread/src/RsimReads.c:56:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
Rsubread/src/LRMchro-event.c:358:2: style: Statements following 'return' will never be executed. [unreachableCode]
Rsubread/src/LRMchro-event.c:22:28: style: Parameter 'ch1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMchro-event.c:22:40: style: Parameter 'ch2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMchro-event.c:32:17: style: Variable 'context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMchro-event.c:33:8: style: Variable 'event_ids' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMchro-event.c:34:15: style: Variable 'body_l' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMchro-event.c:35:15: style: Variable 'body_r' can be declared as pointer to const [constVariablePointer]
Rsubread/src/LRMchro-event.c:127:64: style: Parameter 'order_index' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMchro-event.c:194:147: style: Parameter 'new_event' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMchro-event.c:212:37: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/LRMchro-event.c:221:16: style: Variable 'thise' can be declared as pointer to const [constVariablePointer]
Rsubread/src/RsimReads.c:154:8: style: Condition 'to_display' is always false [knownConditionTrueFalse]
Rsubread/src/RsimReads.c:152:22: note: Assignment 'to_display=0', assigned value is 0
Rsubread/src/RsimReads.c:154:8: note: Condition 'to_display' is always false
Rsubread/src/RsimReads.c:220:9: error: Common realloc mistake: 'lbuf' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/RsimReads.c:207:14: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_name [nullPointerOutOfMemory]
Rsubread/src/RsimReads.c:201:24: note: Assuming allocation function fails
Rsubread/src/RsimReads.c:201:24: note: Assignment 'seq_name=malloc(strlen(clinebuf))', assigned value is 0
Rsubread/src/RsimReads.c:202:22: note: Assuming condition is false
Rsubread/src/RsimReads.c:207:14: note: Null pointer dereference
Rsubread/src/RsimReads.c:275:14: warning: If memory allocation fails, then there is a possible null pointer dereference: qstr [nullPointerOutOfMemory]
Rsubread/src/RsimReads.c:274:27: note: Assuming allocation function fails
Rsubread/src/RsimReads.c:274:27: note: Assignment 'qstr=malloc(rline)', assigned value is 0
Rsubread/src/RsimReads.c:275:14: note: Null pointer dereference
Rsubread/src/RsimReads.c:276:10: warning: If memory allocation fails, then there is a possible null pointer dereference: qstr [nullPointerOutOfMemory]
Rsubread/src/RsimReads.c:274:27: note: Assuming allocation function fails
Rsubread/src/RsimReads.c:274:27: note: Assignment 'qstr=malloc(rline)', assigned value is 0
Rsubread/src/RsimReads.c:276:10: note: Null pointer dereference
Rsubread/src/RsimReads.c:50:62: style: Parameter 'qua' can be declared as pointer to const [constParameterPointer]
Rsubread/src/RsimReads.c:69:10: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
Rsubread/src/RsimReads.c:110:58: style: Parameter 'seq_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/RsimReads.c:117:54: style: Parameter 'fasta_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/RsimReads.c:182:16: style: Variable 'had_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/RsimReads.c:242:12: style: Variable 'had_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/RsimReads.c:314:148: style: Parameter 'start_poses' can be declared as pointer to const [constParameterPointer]
Rsubread/src/RsimReads.c:314:166: style: Parameter 'fra_lens' can be declared as pointer to const [constParameterPointer]
Rsubread/src/RsimReads.c:167:11: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/RsimReads.c:174:11: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/RsimReads.c:204:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/RsimReads.c:215:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/RsimReads.c:235:9: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/RsimReads.c:347:8: style: Variable 'retv' is assigned a value that is never used. [unreadVariable]
Rsubread/src/SNPCalling.c:270:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/SNPCalling.c:1046:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/SNPCalling.c:1545:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/SNPCalling.c:1648:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/atgcContent.c:82:15: warning: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
Rsubread/src/atgcContent.c:81:25: note: Assuming allocation function fails
Rsubread/src/atgcContent.c:81:12: note: Assignment 'line=(char*)calloc(MAX_LINE_LENGTH,1)', assigned value is 0
Rsubread/src/atgcContent.c:82:15: note: Null pointer dereference
Rsubread/src/atgcContent.c:82:38: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
Rsubread/src/atgcContent.c:78:14: note: Assuming allocation function fails
Rsubread/src/atgcContent.c:78:14: note: Assignment 'fin=fopen(*input,"r")', assigned value is 0
Rsubread/src/atgcContent.c:82:38: note: Null pointer dereference
Rsubread/src/atgcContent.c:102:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
Rsubread/src/atgcContent.c:79:15: note: Assuming allocation function fails
Rsubread/src/atgcContent.c:79:15: note: Assignment 'fout=fopen(*output_seq,"w")', assigned value is 0
Rsubread/src/atgcContent.c:102:10: note: Null pointer dereference
Rsubread/src/atgcContent.c:130:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
Rsubread/src/atgcContent.c:128:15: note: Assuming allocation function fails
Rsubread/src/atgcContent.c:128:15: note: Assignment 'fout=fopen(*output,"w")', assigned value is 0
Rsubread/src/atgcContent.c:130:11: note: Null pointer dereference
Rsubread/src/atgcContent.c:131:16: warning: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
Rsubread/src/atgcContent.c:121:23: note: Assuming allocation function fails
Rsubread/src/atgcContent.c:121:10: note: Assignment 'line=(char*)calloc(MAX_LINE_LENGTH,1)', assigned value is 0
Rsubread/src/atgcContent.c:131:16: note: Null pointer dereference
Rsubread/src/atgcContent.c:131:39: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
Rsubread/src/atgcContent.c:127:14: note: Assuming allocation function fails
Rsubread/src/atgcContent.c:127:14: note: Assignment 'fin=fopen(*input,"r")', assigned value is 0
Rsubread/src/atgcContent.c:131:39: note: Null pointer dereference
Rsubread/src/atgcContent.c:32:9: style: Variable 'a' can be declared as pointer to const [constVariablePointer]
Rsubread/src/atgcContent.c:85:11: style: Variable 'flin' can be declared as pointer to const [constVariablePointer]
Rsubread/src/atgcContent.c:105:54: style: Parameter 'basewise' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:2790:2: warning: Return value of function pthread_mutex_trylock() is not used. [ignoredReturnValue]
Rsubread/src/HelperFunctions.c:1979:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/HelperFunctions.c:2811:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/HelperFunctions.c:3007:22: style: Expression is always true because 'else if' condition is opposite to previous condition at line 3002. [multiCondition]
Rsubread/src/HelperFunctions.c:3002:22: note: first condition
Rsubread/src/HelperFunctions.c:3007:22: note: else if condition is opposite to first condition
Rsubread/src/HelperFunctions.c:984:16: style: Return value 'mac_str(str_buff)' is always true [knownConditionTrueFalse]
Rsubread/src/HelperFunctions.c:984:16: note: Calling function 'mac_str' returns 1
Rsubread/src/HelperFunctions.c:984:16: note: Return value 'mac_str(str_buff)' is always true
Rsubread/src/HelperFunctions.c:984:64: style: Return value 'mathrand_str(str_buff)' is always false [knownConditionTrueFalse]
Rsubread/src/HelperFunctions.c:984:64: note: Calling function 'mathrand_str' returns 0
Rsubread/src/HelperFunctions.c:984:64: note: Return value 'mathrand_str(str_buff)' is always false
Rsubread/src/HelperFunctions.c:1253:32: style: Condition 'sam_chr[strlen(sam_chr)-1]=='\r'' is always false [knownConditionTrueFalse]
Rsubread/src/HelperFunctions.c:1252:30: note: Assignment 'sam_chr[strlen(sam_chr)-1]=0', assigned value is 0
Rsubread/src/HelperFunctions.c:1253:32: note: Condition 'sam_chr[strlen(sam_chr)-1]=='\r'' is always false
Rsubread/src/HelperFunctions.c:2177:9: style: Condition '!(res>tmp)' is always true [knownConditionTrueFalse]
Rsubread/src/HelperFunctions.c:2174:9: note: res is assigned 'tmp-1' here.
Rsubread/src/HelperFunctions.c:2177:9: note: Condition '!(res>tmp)' is always true
Rsubread/src/HelperFunctions.c:2177:15: style: Condition 'res>tmp' is always false [knownConditionTrueFalse]
Rsubread/src/HelperFunctions.c:2174:9: note: res is assigned 'tmp-1' here.
Rsubread/src/HelperFunctions.c:2177:15: note: Condition 'res>tmp' is always false
Rsubread/src/HelperFunctions.c:1086:3: error: Memory leak: file_line [memleak]
Rsubread/src/HelperFunctions.c:326:7: error: Common realloc mistake: 'bin_block' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/HelperFunctions.c:1118:30: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1115:36: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1113:29: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1112:11: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1118:30: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1119:30: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1115:36: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1113:29: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1113:19: note: end_ptr is assigned 'strtok_r(NULL,"\t",&token_temp)' here.
Rsubread/src/HelperFunctions.c:1119:30: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1121:16: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1115:36: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1113:29: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1112:11: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1121:16: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1132:15: warning: Either the condition 'strand_str==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1135:18: note: Assuming that condition 'strand_str==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1134:32: note: Assignment to 'strand_str=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1113:19: note: end_ptr is assigned 'strtok_r(NULL,"\t",&token_temp)' here.
Rsubread/src/HelperFunctions.c:1132:15: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1147:14: warning: Either the condition 'start_ptr==NULL' is redundant or there is possible null pointer dereference: feature_type. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1152:18: note: Assuming that condition 'start_ptr==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1148:32: note: Assignment to 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1145:24: note: feature_type is assigned 'strtok_r(NULL,"\t",&token_temp)' here.
Rsubread/src/HelperFunctions.c:1147:14: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1155:31: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1152:37: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1149:30: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1148:12: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1155:31: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1156:31: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1152:37: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1149:30: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1149:20: note: end_ptr is assigned 'strtok_r(NULL,"\t",&token_temp)' here.
Rsubread/src/HelperFunctions.c:1156:31: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1159:17: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/HelperFunctions.c:1152:37: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/HelperFunctions.c:1149:30: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1148:12: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/HelperFunctions.c:1159:17: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1245:24: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: fl [nullPointerOutOfMemory]
Rsubread/src/HelperFunctions.c:1236:20: note: Assuming allocation function fails
Rsubread/src/HelperFunctions.c:1236:20: note: Assignment 'fl=malloc(2000)', assigned value is 0
Rsubread/src/HelperFunctions.c:1245:24: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1255:10: warning: If memory allocation fails, then there is a possible null pointer dereference: anno_chr_buf [nullPointerOutOfMemory]
Rsubread/src/HelperFunctions.c:1254:31: note: Assuming allocation function fails
Rsubread/src/HelperFunctions.c:1254:31: note: Assignment 'anno_chr_buf=malloc(strlen(anno_chr)+1)', assigned value is 0
Rsubread/src/HelperFunctions.c:1255:10: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1257:10: warning: If memory allocation fails, then there is a possible null pointer dereference: sam_chr_buf [nullPointerOutOfMemory]
Rsubread/src/HelperFunctions.c:1256:30: note: Assuming allocation function fails
Rsubread/src/HelperFunctions.c:1256:30: note: Assignment 'sam_chr_buf=malloc(strlen(sam_chr)+1)', assigned value is 0
Rsubread/src/HelperFunctions.c:1257:10: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1271:3: warning: If memory allocation fails, then there is a possible null pointer dereference: *lineptr [nullPointerOutOfMemory]
Rsubread/src/HelperFunctions.c:1270:19: note: Assuming allocation function fails
Rsubread/src/HelperFunctions.c:1270:19: note: Assignment '*lineptr=malloc(linecap)', assigned value is 0
Rsubread/src/HelperFunctions.c:1271:3: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1933:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
Rsubread/src/HelperFunctions.c:1931:20: note: Assuming allocation function fails
Rsubread/src/HelperFunctions.c:1931:20: note: Assignment 'ofp=fopen("/tmp/del4-Rlog.txt","a")', assigned value is 0
Rsubread/src/HelperFunctions.c:1933:10: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1934:9: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
Rsubread/src/HelperFunctions.c:1931:20: note: Assuming allocation function fails
Rsubread/src/HelperFunctions.c:1931:20: note: Assignment 'ofp=fopen("/tmp/del4-Rlog.txt","a")', assigned value is 0
Rsubread/src/HelperFunctions.c:1934:9: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:1991:2: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: obuf [nullPointerOutOfMemory]
Rsubread/src/HelperFunctions.c:1988:22: note: Assuming allocation function fails
Rsubread/src/HelperFunctions.c:1988:22: note: Assignment 'obuf=malloc(3000+1)', assigned value is 0
Rsubread/src/HelperFunctions.c:1991:2: note: Null pointer dereference
Rsubread/src/HelperFunctions.c:2749:18: style: Checking if unsigned expression 'cached_mem' is less than zero. [unsignedLessThanZero]
Rsubread/src/HelperFunctions.c:62:40: style:inconclusive: Function 'sorting_LLU_array_exchange' argument 1 names different: declaration 'arr' definition 'varr'. [funcArgNamesDifferent]
Rsubread/src/HelperFunctions.h:275:40: note: Function 'sorting_LLU_array_exchange' argument 1 names different: declaration 'arr' definition 'varr'.
Rsubread/src/HelperFunctions.c:62:40: note: Function 'sorting_LLU_array_exchange' argument 1 names different: declaration 'arr' definition 'varr'.
Rsubread/src/HelperFunctions.c:69:38: style:inconclusive: Function 'sorting_LLU_array_compare' argument 1 names different: declaration 'arr' definition 'varr'. [funcArgNamesDifferent]
Rsubread/src/HelperFunctions.h:276:38: note: Function 'sorting_LLU_array_compare' argument 1 names different: declaration 'arr' definition 'varr'.
Rsubread/src/HelperFunctions.c:69:38: note: Function 'sorting_LLU_array_compare' argument 1 names different: declaration 'arr' definition 'varr'.
Rsubread/src/HelperFunctions.c:983:28: style:inconclusive: Function 'mac_or_rand_str' argument 1 names different: declaration 'char_14' definition 'str_buff'. [funcArgNamesDifferent]
Rsubread/src/HelperFunctions.h:124:28: note: Function 'mac_or_rand_str' argument 1 names different: declaration 'char_14' definition 'str_buff'.
Rsubread/src/HelperFunctions.c:983:28: note: Function 'mac_or_rand_str' argument 1 names different: declaration 'char_14' definition 'str_buff'.
Rsubread/src/HelperFunctions.c:1029:112: style:inconclusive: Function 'fast_fisher_test_one_side' argument 5 names different: declaration 'frac_buffer' definition 'buff'. [funcArgNamesDifferent]
Rsubread/src/HelperFunctions.h:126:112: note: Function 'fast_fisher_test_one_side' argument 5 names different: declaration 'frac_buffer' definition 'buff'.
Rsubread/src/HelperFunctions.c:1029:112: note: Function 'fast_fisher_test_one_side' argument 5 names different: declaration 'frac_buffer' definition 'buff'.
Rsubread/src/HelperFunctions.c:1029:122: style:inconclusive: Function 'fast_fisher_test_one_side' argument 6 names different: declaration 'buffer_size' definition 'buflen'. [funcArgNamesDifferent]
Rsubread/src/HelperFunctions.h:126:129: note: Function 'fast_fisher_test_one_side' argument 6 names different: declaration 'buffer_size' definition 'buflen'.
Rsubread/src/HelperFunctions.c:1029:122: note: Function 'fast_fisher_test_one_side' argument 6 names different: declaration 'buffer_size' definition 'buflen'.
Rsubread/src/HelperFunctions.c:2126:54: style:inconclusive: Function 'TNbignum_to_string' argument 3 names different: declaration 'maxsize' definition 'nbytes'. [funcArgNamesDifferent]
Rsubread/src/HelperFunctions.h:246:54: note: Function 'TNbignum_to_string' argument 3 names different: declaration 'maxsize' definition 'nbytes'.
Rsubread/src/HelperFunctions.c:2126:54: note: Function 'TNbignum_to_string' argument 3 names different: declaration 'maxsize' definition 'nbytes'.
Rsubread/src/HelperFunctions.c:1090:49: style: Local variable 'is_negative_strand' shadows outer argument [shadowArgument]
Rsubread/src/HelperFunctions.c:1078:139: note: Shadowed declaration
Rsubread/src/HelperFunctions.c:1090:49: note: Shadow variable
Rsubread/src/HelperFunctions.c:1091:70: style: Local variable 'chro_name' shadows outer argument [shadowArgument]
Rsubread/src/HelperFunctions.c:1078:86: note: Shadowed declaration
Rsubread/src/HelperFunctions.c:1091:70: note: Shadow variable
Rsubread/src/HelperFunctions.c:1095:16: style: Local variable 'start' shadows outer argument [shadowArgument]
Rsubread/src/HelperFunctions.c:1078:110: note: Shadowed declaration
Rsubread/src/HelperFunctions.c:1095:16: note: Shadow variable
Rsubread/src/HelperFunctions.c:1095:27: style: Local variable 'end' shadows outer argument [shadowArgument]
Rsubread/src/HelperFunctions.c:1078:130: note: Shadowed declaration
Rsubread/src/HelperFunctions.c:1095:27: note: Shadow variable
Rsubread/src/HelperFunctions.c:70:13: style: Variable 'arr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:76:32: style: Parameter 'keyword' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:82:10: style: Variable 'rret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:198:65: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:235:40: style: Parameter 'tab' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:235:52: style: Parameter 'chro' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:239:11: style: Variable 'bin_block' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:261:53: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:309:13: style: Variable 'mem_chro' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:655:9: style: Variable 'extra_column' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:740:10: style: Variable 'ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:757:37: style: Parameter 'rep' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:757:48: style: Parameter 'with' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:802:26: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:802:37: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:861:20: style: Parameter 'str_buff' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:1011:37: style: Parameter 'tab' can be declared as const array [constParameter]
Rsubread/src/HelperFunctions.c:1077:122: style: Parameter 'used_feature_type' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:1112:11: style: Variable 'start_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1113:11: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1134:11: style: Variable 'strand_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1145:11: style: Variable 'feature_type' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1148:12: style: Variable 'start_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1149:12: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1245:9: style: Variable 'ret_fl' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1249:10: style: Variable 'anno_chr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/HelperFunctions.c:1530:27: style: Parameter 'plain_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:1794:30: style: Parameter 'plain_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:1880:16: style: Variable 'a' can be declared as const array [constVariable]
Rsubread/src/HelperFunctions.c:1881:16: style: Variable 'b' can be declared as const array [constVariable]
Rsubread/src/HelperFunctions.c:1882:16: style: Variable 'c' can be declared as const array [constVariable]
Rsubread/src/HelperFunctions.c:1883:16: style: Variable 'd' can be declared as const array [constVariable]
Rsubread/src/HelperFunctions.c:2922:34: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:2923:27: style: Parameter 'penalties' can be declared as pointer to const [constParameterPointer]
Rsubread/src/HelperFunctions.c:157:23: warning: Uninitialized variable: jump_mode [uninitvar]
Rsubread/src/HelperFunctions.c:147:28: note: Assuming condition is false
Rsubread/src/HelperFunctions.c:157:23: note: Uninitialized variable: jump_mode
Rsubread/src/HelperFunctions.c:805:10: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/HelperFunctions.c:2845:14: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
Rsubread/src/HelperFunctions.c:2887:21: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
Rsubread/src/cell-counts.c:495:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/cell-counts.c:638:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/cell-counts.c:738:112: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/cell-counts.c:2749:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable votes [valueFlowBailoutIncompleteVar]
Rsubread/src/cell-counts.c:4871:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LC_ALL [valueFlowBailoutIncompleteVar]
Rsubread/src/core-bigtable.c:275:11: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:275:11: note: Null pointer dereference
Rsubread/src/core-bigtable.c:277:4: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:277:4: note: Null pointer dereference
Rsubread/src/core-bigtable.c:278:4: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:278:4: note: Null pointer dereference
Rsubread/src/core-bigtable.c:279:4: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:279:4: note: Null pointer dereference
Rsubread/src/core-bigtable.c:280:4: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:280:4: note: Null pointer dereference
Rsubread/src/core-bigtable.c:281:4: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:281:4: note: Null pointer dereference
Rsubread/src/core-bigtable.c:284:11: warning: If memory allocation fails, then there is a possible null pointer dereference: dynamic_key [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:283:31: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:283:31: note: Assignment 'dynamic_key=malloc(strlen(static_key)+1)', assigned value is 0
Rsubread/src/core-bigtable.c:284:11: note: Null pointer dereference
Rsubread/src/core-bigtable.c:287:6: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:287:6: note: Null pointer dereference
Rsubread/src/core-bigtable.c:287:31: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
Rsubread/src/core-bigtable.c:287:31: note: Null pointer dereference
Rsubread/src/core-bigtable.c:84:66: style:inconclusive: Function 'init_bigtable_results' argument 2 names different: declaration 'is_rewind' definition 'is_rewinding'. [funcArgNamesDifferent]
Rsubread/src/core-bigtable.h:14:66: note: Function 'init_bigtable_results' argument 2 names different: declaration 'is_rewind' definition 'is_rewinding'.
Rsubread/src/core-bigtable.c:84:66: note: Function 'init_bigtable_results' argument 2 names different: declaration 'is_rewind' definition 'is_rewinding'.
Rsubread/src/core-bigtable.c:302:31: style:inconclusive: Function 'bktable_free_ptrs' argument 1 names different: declaration 'bkey' definition 'bukey'. [funcArgNamesDifferent]
Rsubread/src/core-bigtable.h:39:31: note: Function 'bktable_free_ptrs' argument 1 names different: declaration 'bkey' definition 'bukey'.
Rsubread/src/core-bigtable.c:302:31: note: Function 'bktable_free_ptrs' argument 1 names different: declaration 'bkey' definition 'bukey'.
Rsubread/src/core-bigtable.c:29:60: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-bigtable.c:75:30: style: Variable 'rett' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-bigtable.c:143:53: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-bigtable.c:149:39: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-bigtable.c:161:107: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-bigtable.c:171:29: style: Variable 'cache' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-bigtable.c:183:29: style: Variable 'cache' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-bigtable.c:188:49: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-bigtable.c:188:85: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-bigtable.c:315:39: style: Parameter 'tab' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-bigtable.c:189:14: warning: String literal compared with variable 'NULL'. Did you intend to use strcmp() instead? [literalWithCharPtrCompare]
Rsubread/src/SNPCalling.c:1532:3: warning:inconclusive: The buffer 'old_read_name' may not be null-terminated after the call to strncpy(). [terminateStrncpy]
Rsubread/src/SNPCalling.c:1350:20: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
Rsubread/src/SNPCalling.c:527:10: style: Condition '0&&chro_pos<16084550+12' is always false [knownConditionTrueFalse]
Rsubread/src/SNPCalling.c:559:10: style: Condition '0&&strcmp("8",chro_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/SNPCalling.c:565:10: style: Condition '0&&chro_pos<16084550+12' is always false [knownConditionTrueFalse]
Rsubread/src/SNPCalling.c:571:33: style: Condition '0&&Known_SNP_here' is always false [knownConditionTrueFalse]
Rsubread/src/SNPCalling.c:697:114: style: Condition 'parameters->fisher_exact_testlen||parameters->test_two_strands||parameters->neighbour_abundance_test||1' is always true [knownConditionTrueFalse]
Rsubread/src/SNPCalling.c:1031:12: style: Condition '1||all_offset<=chro_len-1' is always true [knownConditionTrueFalse]
Rsubread/src/SNPCalling.c:918:6: warning: %d in format string (no. 7) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/SNPCalling.c:651:3: error: Memory leak: snp_voting_piles [memleak]
Rsubread/src/SNPCalling.c:651:3: error: Memory leak: pcutoff_list [memleak]
Rsubread/src/SNPCalling.c:651:3: error: Memory leak: snp_filter_background_unmatched [memleak]
Rsubread/src/SNPCalling.c:651:3: error: Memory leak: snp_filter_background_matched [memleak]
Rsubread/src/SNPCalling.c:651:3: error: Memory leak: sprint_line [memleak]
Rsubread/src/SNPCalling.c:636:2: warning: If memory allocation fails, then there is a possible null pointer dereference: sprint_line [nullPointerOutOfMemory]
Rsubread/src/SNPCalling.c:635:22: note: Assuming allocation function fails
Rsubread/src/SNPCalling.c:635:22: note: Assignment 'sprint_line=malloc(1000)', assigned value is 0
Rsubread/src/SNPCalling.c:636:2: note: Null pointer dereference
Rsubread/src/SNPCalling.c:674:10: warning: If memory allocation fails, then there is a possible null pointer dereference: snp_BGC_piles [nullPointerOutOfMemory]
Rsubread/src/SNPCalling.c:671:35: note: Assuming allocation function fails
Rsubread/src/SNPCalling.c:671:19: note: Assignment 'snp_BGC_piles=(unsigned int*)malloc(sizeof(unsigned int)*reference_len*4)', assigned value is 0
Rsubread/src/SNPCalling.c:674:10: note: Null pointer dereference
Rsubread/src/SNPCalling.c:675:10: warning: If memory allocation fails, then there is a possible null pointer dereference: snp_fisher_BGC [nullPointerOutOfMemory]
Rsubread/src/SNPCalling.c:672:29: note: Assuming allocation function fails
Rsubread/src/SNPCalling.c:672:20: note: Assignment 'snp_fisher_BGC=(float*)malloc(sizeof(float)*reference_len)', assigned value is 0
Rsubread/src/SNPCalling.c:675:10: note: Null pointer dereference
Rsubread/src/SNPCalling.c:676:10: warning: If memory allocation fails, then there is a possible null pointer dereference: snp_fisher_VS [nullPointerOutOfMemory]
Rsubread/src/SNPCalling.c:673:28: note: Assuming allocation function fails
Rsubread/src/SNPCalling.c:673:19: note: Assignment 'snp_fisher_VS=(float*)malloc(sizeof(float)*reference_len)', assigned value is 0
Rsubread/src/SNPCalling.c:676:10: note: Null pointer dereference
Rsubread/src/SNPCalling.c:687:10: warning: Either the condition 'tmp_fp' is redundant or there is possible null pointer dereference: tmp_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:680:6: note: Assuming that condition 'tmp_fp' is not redundant
Rsubread/src/SNPCalling.c:687:10: note: Null pointer dereference
Rsubread/src/SNPCalling.c:700:10: warning: If memory allocation fails, then there is a possible null pointer dereference: base_is_reliable [nullPointerOutOfMemory]
Rsubread/src/SNPCalling.c:699:36: note: Assuming allocation function fails
Rsubread/src/SNPCalling.c:699:22: note: Assignment 'base_is_reliable=(char*)malloc(sizeof(char)*reference_len)', assigned value is 0
Rsubread/src/SNPCalling.c:700:10: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1129:36: warning: Either the condition '!fp' is redundant or there is possible null pointer dereference: fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1131:5: note: Assuming that condition '!fp' is not redundant
Rsubread/src/SNPCalling.c:1129:36: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1199:33: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1199:33: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1200:10: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1200:10: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1201:227: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1201:227: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1202:77: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1202:77: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1203:128: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1203:128: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1204:126: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1204:126: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1205:135: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1205:135: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1206:106: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1206:106: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1207:110: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1207:110: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1208:59: warning: Either the condition '!out_fp' is redundant or there is possible null pointer dereference: out_fp. [nullPointerRedundantCheck]
Rsubread/src/SNPCalling.c:1196:5: note: Assuming that condition '!out_fp' is not redundant
Rsubread/src/SNPCalling.c:1208:59: note: Null pointer dereference
Rsubread/src/SNPCalling.c:1393:3: warning: If memory allocation fails, then there is a possible null pointer dereference: precalculated_factorial [nullPointerOutOfMemory]
Rsubread/src/SNPCalling.c:1391:48: note: Assuming allocation function fails
Rsubread/src/SNPCalling.c:1391:28: note: Assignment 'precalculated_factorial=(long double*)malloc(sizeof(long double)*2000000*2)', assigned value is 0
Rsubread/src/SNPCalling.c:1393:3: note: Null pointer dereference
Rsubread/src/SNPCalling.c:303:8: style: Local variable 'rlen' shadows outer variable [shadowVariable]
Rsubread/src/SNPCalling.c:269:34: note: Shadowed declaration
Rsubread/src/SNPCalling.c:303:8: note: Shadow variable
Rsubread/src/SNPCalling.c:765:17: style: Local variable 'reference_len_long' shadows outer variable [shadowVariable]
Rsubread/src/SNPCalling.c:622:16: note: Shadowed declaration
Rsubread/src/SNPCalling.c:765:17: note: Shadow variable
Rsubread/src/SNPCalling.c:210:26: style: Parameter 'bm' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:259:190: style: Parameter 'referenced_genome' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:451:83: style: Parameter 'snp_voting_piles' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:461:163: style: Parameter 'referenced_genome' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:461:219: style: Parameter 'tumor_P' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:484:111: style: Parameter 'snp_voting_piles' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:484:136: style: Parameter 'referenced_genome' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:959:13: style: Variable 'ins_seq' can be declared as pointer to const [constVariablePointer]
Rsubread/src/SNPCalling.c:966:22: style: Variable 'indel_sups' can be declared as pointer to const [constVariablePointer]
Rsubread/src/SNPCalling.c:1102:11: style: Variable 'ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/SNPCalling.c:1376:24: style: Parameter 'in_SAM_file' can be declared as pointer to const [constParameterPointer]
Rsubread/src/SNPCalling.c:1528:35: error: Uninitialized variable: old_read_name [uninitvar]
Rsubread/src/SNPCalling.c:487:17: style: Variable 'POIbase_MM' is assigned a value that is never used. [unreadVariable]
Rsubread/src/SNPCalling.c:487:46: style: Variable 'POIbase_MAT' is assigned a value that is never used. [unreadVariable]
Rsubread/src/SNPCalling.c:707:17: style: Variable 'window_no' is assigned a value that is never used. [unreadVariable]
Rsubread/src/SNPCalling.c:715:15: style: Variable 'window_no' is assigned a value that is never used. [unreadVariable]
Rsubread/src/SNPCalling.c:721:15: style: Variable 'window_no' is assigned a value that is never used. [unreadVariable]
Rsubread/src/SNPCalling.c:764:8: style: Variable 'a' is assigned a value that is never used. [unreadVariable]
Rsubread/src/SNPCalling.c:764:18: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-interface-aligner.c:80:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/core-interface-aligner.c:262:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:337:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable current_max_event_number [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:950:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_space_dynamic [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:1059:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_space_dynamic [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:1505:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_space_dynamic [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:1844:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:2724:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable total_events [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:2834:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:3663:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable total_events [valueFlowBailoutIncompleteVar]
Rsubread/src/cell-counts.c:4327:2: error: Address of local auto-variable assigned to a function parameter. [autoVariables]
Rsubread/src/cell-counts.c:2810:2: error: Buffer is accessed out of bounds: vote->items [bufferAccessOutOfBounds]
Rsubread/src/cell-counts.c:2916:3: error: Buffer is accessed out of bounds: vote->items [bufferAccessOutOfBounds]
Rsubread/src/cell-counts.c:3824:4: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/cell-counts.c:3830:4: warning: Return value of function deflate() is not used. [ignoredReturnValue]
Rsubread/src/cell-counts.c:391:30: warning: Identical condition 'last_matched_base_index<0', second condition is always false [identicalConditionAfterEarlyExit]
Rsubread/src/cell-counts.c:388:29: note: If condition 'last_matched_base_index<0' is true, the function will return/exit
Rsubread/src/cell-counts.c:391:30: note: Testing identical condition 'last_matched_base_index<0'
Rsubread/src/cell-counts.c:394:30: style: Condition 'last_matched_base_index>=0' is always true [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:388:29: note: Assuming that condition 'last_matched_base_index<0' is not redundant
Rsubread/src/cell-counts.c:394:30: note: Condition 'last_matched_base_index>=0' is always true
Rsubread/src/cell-counts.c:2373:7: style: Condition '0&&FIXLENstrcmp("R00001325252",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:2436:7: style: Condition '0&&FIXLENstrcmp("R00000000057",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:2553:7: style: Condition '0&&FIXLENstrcmp("R00000075029",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:2564:8: style: Condition '0&&FIXLENstrcmp("R00000075029",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:2587:8: style: Condition '0&&FIXLENstrcmp("R00000075029",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:2634:7: style: Condition '0&&(FIXLENstrcmp("R00000002478",read_name)==0||rebuilt_rlen!=read_len)' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:2908:7: style: Condition '0&&FIXLENstrcmp("R00004925364",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:2974:12: style: Condition '0&&FIXLENstrcmp("R00004925364",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/cell-counts.c:3082:3: error: Memory leak: read_text [memleak]
Rsubread/src/cell-counts.c:3082:3: error: Memory leak: qual_text [memleak]
Rsubread/src/cell-counts.c:3181:3: error: Memory leak: read_text [memleak]
Rsubread/src/cell-counts.c:3181:3: error: Memory leak: qual_text [memleak]
Rsubread/src/cell-counts.c:509:4: error: Common realloc mistake: 'cmd_rebuilt' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:728:4: error: Common realloc mistake: 'outbuff' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:1226:6: error: Common realloc mistake: 'ret_block_min_start' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:1227:6: error: Common realloc mistake: 'ret_block_max_end' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:1228:6: error: Common realloc mistake: 'ret_block_end_index' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:1249:5: error: Common realloc mistake: 'ret_block_min_start' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:1250:5: error: Common realloc mistake: 'ret_block_max_end' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:1251:5: error: Common realloc mistake: 'ret_block_end_index' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:4018:5: error: Common realloc mistake: 'bin_ptrs' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/cell-counts.c:275:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:816:42: note: Calling function 'cellCounts_make_barcode_HT_table', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:275:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:276:36: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:816:42: note: Calling function 'cellCounts_make_barcode_HT_table', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:276:36: note: Null pointer dereference
Rsubread/src/cell-counts.c:278:18: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:816:42: note: Calling function 'cellCounts_make_barcode_HT_table', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:278:18: note: Null pointer dereference
Rsubread/src/cell-counts.c:279:28: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:816:42: note: Calling function 'cellCounts_make_barcode_HT_table', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:279:28: note: Null pointer dereference
Rsubread/src/cell-counts.c:281:6: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:816:42: note: Calling function 'cellCounts_make_barcode_HT_table', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:281:6: note: Null pointer dereference
Rsubread/src/cell-counts.c:282:11: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:816:42: note: Calling function 'cellCounts_make_barcode_HT_table', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:282:11: note: Null pointer dereference
Rsubread/src/cell-counts.c:288:16: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:816:42: note: Calling function 'cellCounts_make_barcode_HT_table', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:282:9: note: Assuming condition is false
Rsubread/src/cell-counts.c:288:16: note: Null pointer dereference
Rsubread/src/cell-counts.c:502:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cmd_rebuilt [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:500:29: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:500:29: note: Assignment 'cmd_rebuilt=malloc(cmd_rebuilt_size)', assigned value is 0
Rsubread/src/cell-counts.c:502:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:505:32: warning: If memory allocation fails, then there is a possible null pointer dereference: cmd_rebuilt [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:500:29: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:500:29: note: Assignment 'cmd_rebuilt=malloc(cmd_rebuilt_size)', assigned value is 0
Rsubread/src/cell-counts.c:505:32: note: Null pointer dereference
Rsubread/src/cell-counts.c:514:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:514:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:515:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:515:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:516:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:516:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:517:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:517:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:518:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:518:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:519:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:519:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:520:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:520:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:523:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:523:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:524:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:524:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:525:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:525:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:526:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:526:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:527:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:527:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:528:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:528:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:528:49: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:528:49: note: Null pointer dereference
Rsubread/src/cell-counts.c:529:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:529:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:530:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:530:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:531:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:531:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:532:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:532:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:533:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:533:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:543:9: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:543:9: note: Null pointer dereference
Rsubread/src/cell-counts.c:655:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1399:42: note: Calling function 'determine_total_index_blocks', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:655:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:657:72: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1399:42: note: Calling function 'determine_total_index_blocks', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:657:72: note: Null pointer dereference
Rsubread/src/cell-counts.c:657:99: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1399:42: note: Calling function 'determine_total_index_blocks', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:657:99: note: Null pointer dereference
Rsubread/src/cell-counts.c:659:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1399:42: note: Calling function 'determine_total_index_blocks', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:658:6: note: Assuming condition is false
Rsubread/src/cell-counts.c:659:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:661:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1399:42: note: Calling function 'determine_total_index_blocks', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:658:6: note: Assuming condition is false
Rsubread/src/cell-counts.c:661:5: note: Null pointer dereference
Rsubread/src/cell-counts.c:681:3: warning: If memory allocation fails, then there is a possible null pointer dereference: push_arr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:676:28: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:676:28: note: Assignment 'push_arr=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:681:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:682:3: warning: If memory allocation fails, then there is a possible null pointer dereference: push_arr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:676:28: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:676:28: note: Assignment 'push_arr=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:682:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:683:3: warning: If memory allocation fails, then there is a possible null pointer dereference: push_arr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:676:28: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:676:28: note: Assignment 'push_arr=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:683:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:684:3: warning: If memory allocation fails, then there is a possible null pointer dereference: push_arr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:676:28: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:676:28: note: Assignment 'push_arr=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:684:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:739:2: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: outbuff [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:722:25: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:722:25: note: Assignment 'outbuff=malloc(outcapa)', assigned value is 0
Rsubread/src/cell-counts.c:725:13: note: Assuming condition is false
Rsubread/src/cell-counts.c:739:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:740:2: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: outbuff [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:722:25: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:722:25: note: Assignment 'outbuff=malloc(outcapa)', assigned value is 0
Rsubread/src/cell-counts.c:725:13: note: Assuming condition is false
Rsubread/src/cell-counts.c:740:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:795:4: warning: If memory allocation fails, then there is a possible null pointer dereference: wtrptr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:794:27: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:794:27: note: Assignment 'wtrptr=malloc(sizeof(void*)*6)', assigned value is 0
Rsubread/src/cell-counts.c:795:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:796:4: warning: If memory allocation fails, then there is a possible null pointer dereference: wtrptr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:794:27: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:794:27: note: Assignment 'wtrptr=malloc(sizeof(void*)*6)', assigned value is 0
Rsubread/src/cell-counts.c:796:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:797:4: warning: If memory allocation fails, then there is a possible null pointer dereference: wtrptr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:794:27: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:794:27: note: Assignment 'wtrptr=malloc(sizeof(void*)*6)', assigned value is 0
Rsubread/src/cell-counts.c:797:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:798:4: warning: If memory allocation fails, then there is a possible null pointer dereference: wtrptr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:794:27: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:794:27: note: Assignment 'wtrptr=malloc(sizeof(void*)*6)', assigned value is 0
Rsubread/src/cell-counts.c:798:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:799:4: warning: If memory allocation fails, then there is a possible null pointer dereference: wtrptr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:794:27: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:794:27: note: Assignment 'wtrptr=malloc(sizeof(void*)*6)', assigned value is 0
Rsubread/src/cell-counts.c:799:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:800:4: warning: If memory allocation fails, then there is a possible null pointer dereference: wtrptr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:794:27: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:794:27: note: Assignment 'wtrptr=malloc(sizeof(void*)*6)', assigned value is 0
Rsubread/src/cell-counts.c:800:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:810:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:810:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:810:68: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:810:68: note: Null pointer dereference
Rsubread/src/cell-counts.c:811:13: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:811:13: note: Null pointer dereference
Rsubread/src/cell-counts.c:852:72: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1403:48: note: Calling function 'cellCounts_load_base_value_indexes', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:852:72: note: Null pointer dereference
Rsubread/src/cell-counts.c:853:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1403:48: note: Calling function 'cellCounts_load_base_value_indexes', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:853:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:854:26: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1403:48: note: Calling function 'cellCounts_load_base_value_indexes', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:854:26: note: Null pointer dereference
Rsubread/src/cell-counts.c:931:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:931:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:932:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:932:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:932:104: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:932:104: note: Null pointer dereference
Rsubread/src/cell-counts.c:933:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:933:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:934:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:934:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:935:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:935:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:936:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:936:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:946:3: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:943:21: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:943:21: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:946:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:947:3: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:943:21: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:943:21: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:947:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:948:3: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:943:21: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:943:21: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:948:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:949:3: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:943:21: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:943:21: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:949:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:952:2: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:943:21: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:943:21: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:952:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:954:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:943:21: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:943:21: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:954:5: note: Null pointer dereference
Rsubread/src/cell-counts.c:1057:27: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_start [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1025:31: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1025:31: note: Assignment 'tmp_start=malloc(sizeof(long long)*total_items)', assigned value is 0
Rsubread/src/cell-counts.c:1057:27: note: Null pointer dereference
Rsubread/src/cell-counts.c:1058:25: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_end [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1026:29: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1026:29: note: Assignment 'tmp_end=malloc(sizeof(long long)*total_items)', assigned value is 0
Rsubread/src/cell-counts.c:1058:25: note: Null pointer dereference
Rsubread/src/cell-counts.c:1059:28: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_strand [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1027:37: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1027:37: note: Assignment 'tmp_strand=malloc(sizeof(char)*total_items)', assigned value is 0
Rsubread/src/cell-counts.c:1059:28: note: Null pointer dereference
Rsubread/src/cell-counts.c:1060:29: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_entyrez [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1028:28: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1028:28: note: Assignment 'tmp_entyrez=malloc(sizeof(int)*total_items)', assigned value is 0
Rsubread/src/cell-counts.c:1060:29: note: Null pointer dereference
Rsubread/src/cell-counts.c:1061:30: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_info_ptr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1029:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1029:44: note: Assignment 'tmp_info_ptr=malloc(sizeof(struct fc_feature_info_t*)*total_items)', assigned value is 0
Rsubread/src/cell-counts.c:1061:30: note: Null pointer dereference
Rsubread/src/cell-counts.c:1280:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1405:41: note: Calling function 'cellCounts_load_annotations', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1280:5: note: Null pointer dereference
Rsubread/src/cell-counts.c:1295:4: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:1295:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:1296:4: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:1296:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:1298:4: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:1298:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:1298:50: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:1298:50: note: Null pointer dereference
Rsubread/src/cell-counts.c:1299:4: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:1299:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:1299:53: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/cell-counts.c:1299:53: note: Null pointer dereference
Rsubread/src/cell-counts.c:1338:88: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1406:44: note: Calling function 'cellCounts_open_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1338:88: note: Null pointer dereference
Rsubread/src/cell-counts.c:1339:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1406:44: note: Calling function 'cellCounts_open_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1339:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:1340:24: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1406:44: note: Calling function 'cellCounts_open_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1340:24: note: Null pointer dereference
Rsubread/src/cell-counts.c:1343:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1406:44: note: Calling function 'cellCounts_open_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1343:5: note: Null pointer dereference
Rsubread/src/cell-counts.c:1359:21: warning: If memory allocation fails, then there is a possible null pointer dereference: lock [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:788:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:788:40: note: Assignment 'gzfp_lock=malloc(sizeof(cellCounts_lock_t))', assigned value is 0
Rsubread/src/cell-counts.c:789:23: note: Calling function 'cellCounts_init_lock', 1st argument 'gzfp_lock' value is 0
Rsubread/src/cell-counts.c:1359:21: note: Null pointer dereference
Rsubread/src/cell-counts.c:1389:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1389:5: note: Null pointer dereference
Rsubread/src/cell-counts.c:1398:61: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1398:61: note: Null pointer dereference
Rsubread/src/cell-counts.c:1402:15: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1402:15: note: Null pointer dereference
Rsubread/src/cell-counts.c:1414:15: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1414:15: note: Null pointer dereference
Rsubread/src/cell-counts.c:1416:27: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1416:27: note: Null pointer dereference
Rsubread/src/cell-counts.c:1419:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1419:5: note: Null pointer dereference
Rsubread/src/cell-counts.c:1431:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1431:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1432:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1432:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1433:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1433:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1434:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1434:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1435:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1435:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1436:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1436:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1437:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1437:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1438:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1438:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1439:19: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1439:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:1440:18: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1440:18: note: Null pointer dereference
Rsubread/src/cell-counts.c:1441:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1441:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1442:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1442:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1443:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1443:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1444:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1444:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1445:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1445:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1446:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1446:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1447:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1447:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1448:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1448:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1449:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1449:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1450:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1450:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1451:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1451:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1452:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1452:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:1453:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4880:42: note: Calling function 'cellCounts_destroy_context', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:1453:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:2149:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thread_contexts [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2143:54: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2143:54: note: Assignment 'thread_contexts=calloc(sizeof(struct cellcounts_align_thread_t),cct_context->total_threads)', assigned value is 0
Rsubread/src/cell-counts.c:2149:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:2154:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thr_parameters [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2153:34: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2153:34: note: Assignment 'thr_parameters=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:2154:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:2155:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thr_parameters [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2153:34: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2153:34: note: Assignment 'thr_parameters=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:2155:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:2156:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thr_parameters [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2153:34: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2153:34: note: Assignment 'thr_parameters=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:2156:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:2157:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thr_parameters [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2153:34: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2153:34: note: Assignment 'thr_parameters=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:2157:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:2159:19: warning: If memory allocation fails, then there is a possible null pointer dereference: thread_contexts [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2143:54: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2143:54: note: Assignment 'thread_contexts=calloc(sizeof(struct cellcounts_align_thread_t),cct_context->total_threads)', assigned value is 0
Rsubread/src/cell-counts.c:2159:19: note: Null pointer dereference
Rsubread/src/cell-counts.c:2163:16: warning: If memory allocation fails, then there is a possible null pointer dereference: thread_contexts [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2143:54: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2143:54: note: Assignment 'thread_contexts=calloc(sizeof(struct cellcounts_align_thread_t),cct_context->total_threads)', assigned value is 0
Rsubread/src/cell-counts.c:2163:16: note: Null pointer dereference
Rsubread/src/cell-counts.c:2164:32: warning: If memory allocation fails, then there is a possible null pointer dereference: thread_contexts [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2143:54: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2143:54: note: Assignment 'thread_contexts=calloc(sizeof(struct cellcounts_align_thread_t),cct_context->total_threads)', assigned value is 0
Rsubread/src/cell-counts.c:2164:32: note: Null pointer dereference
Rsubread/src/cell-counts.c:2165:32: warning: If memory allocation fails, then there is a possible null pointer dereference: thread_contexts [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:2143:54: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:2143:54: note: Assignment 'thread_contexts=calloc(sizeof(struct cellcounts_align_thread_t),cct_context->total_threads)', assigned value is 0
Rsubread/src/cell-counts.c:2165:32: note: Null pointer dereference
Rsubread/src/cell-counts.c:3295:62: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3295:62: note: Null pointer dereference
Rsubread/src/cell-counts.c:3297:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp_out [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:3296:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3296:23: note: Assignment 'fp_out=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:3297:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:3299:67: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3299:67: note: Null pointer dereference
Rsubread/src/cell-counts.c:3300:68: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3300:68: note: Null pointer dereference
Rsubread/src/cell-counts.c:3301:66: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3301:66: note: Null pointer dereference
Rsubread/src/cell-counts.c:3302:64: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3302:64: note: Null pointer dereference
Rsubread/src/cell-counts.c:3303:51: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3303:51: note: Null pointer dereference
Rsubread/src/cell-counts.c:3304:36: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3304:36: note: Null pointer dereference
Rsubread/src/cell-counts.c:3306:21: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3306:21: note: Null pointer dereference
Rsubread/src/cell-counts.c:3307:17: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3307:17: note: Null pointer dereference
Rsubread/src/cell-counts.c:3308:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3299:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3299:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),cct_context->gene_name_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3308:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3313:22: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3313:22: note: Null pointer dereference
Rsubread/src/cell-counts.c:3314:34: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3299:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3299:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),cct_context->gene_name_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3314:34: note: Null pointer dereference
Rsubread/src/cell-counts.c:3316:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3299:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3299:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),cct_context->gene_name_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3316:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3320:21: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3320:21: note: Null pointer dereference
Rsubread/src/cell-counts.c:3321:17: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3321:17: note: Null pointer dereference
Rsubread/src/cell-counts.c:3322:24: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3299:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3299:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),cct_context->gene_name_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3322:24: note: Null pointer dereference
Rsubread/src/cell-counts.c:3322:53: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_pointer [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3300:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3300:44: note: Assignment 'gene_exons_pointer=calloc(sizeof(unsigned int),cct_context->gene_name_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3322:53: note: Null pointer dereference
Rsubread/src/cell-counts.c:3324:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_chr [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3303:33: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3303:33: note: Assignment 'gene_exons_chr=malloc(sizeof(char*)*cct_context->all_features_array->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3324:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3324:36: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3324:36: note: Null pointer dereference
Rsubread/src/cell-counts.c:3325:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_start [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3301:42: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3301:42: note: Assignment 'gene_exons_start=malloc(sizeof(unsigned int)*cct_context->all_features_array->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3325:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3325:38: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3325:38: note: Null pointer dereference
Rsubread/src/cell-counts.c:3326:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_end [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3302:40: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3302:40: note: Assignment 'gene_exons_end=malloc(sizeof(unsigned int)*cct_context->all_features_array->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3326:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3326:36: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3326:36: note: Null pointer dereference
Rsubread/src/cell-counts.c:3327:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_strand [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3304:35: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3304:35: note: Assignment 'gene_exons_strand=malloc(cct_context->all_features_array->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3327:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3327:39: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3327:39: note: Null pointer dereference
Rsubread/src/cell-counts.c:3329:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_pointer [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3300:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3300:44: note: Assignment 'gene_exons_pointer=calloc(sizeof(unsigned int),cct_context->gene_name_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3329:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3337:55: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3337:55: note: Null pointer dereference
Rsubread/src/cell-counts.c:3342:22: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3342:22: note: Null pointer dereference
Rsubread/src/cell-counts.c:3345:10: warning: If memory allocation fails, then there is a possible null pointer dereference: is_occupied [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3332:28: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3332:28: note: Assignment 'is_occupied=malloc(longest_gene_exons)', assigned value is 0
Rsubread/src/cell-counts.c:3345:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:3345:24: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_pointer [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3300:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3300:44: note: Assignment 'gene_exons_pointer=calloc(sizeof(unsigned int),cct_context->gene_name_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:3345:24: note: Null pointer dereference
Rsubread/src/cell-counts.c:3350:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_chr_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3337:30: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3337:30: note: Assignment 'out_chr_list=malloc(longest_gene_exons*(1+cct_context->longest_chro_name)+1)', assigned value is 0
Rsubread/src/cell-counts.c:3350:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3351:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_start_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3338:32: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3338:32: note: Assignment 'out_start_list=malloc(11*longest_gene_exons+1)', assigned value is 0
Rsubread/src/cell-counts.c:3351:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3352:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_end_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3339:30: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3339:30: note: Assignment 'out_end_list=malloc(11*longest_gene_exons+1)', assigned value is 0
Rsubread/src/cell-counts.c:3352:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3353:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_strand_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3340:33: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3340:33: note: Assignment 'out_strand_list=malloc(2*longest_gene_exons+1)', assigned value is 0
Rsubread/src/cell-counts.c:3353:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:3356:33: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4856:42: note: Calling function 'cellCounts_write_gene_list', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3356:33: note: Null pointer dereference
Rsubread/src/cell-counts.c:3358:8: warning: If memory allocation fails, then there is a possible null pointer dereference: is_occupied [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3332:28: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3332:28: note: Assignment 'is_occupied=malloc(longest_gene_exons)', assigned value is 0
Rsubread/src/cell-counts.c:3358:8: note: Null pointer dereference
Rsubread/src/cell-counts.c:3444:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3444:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:3445:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3445:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:3446:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3446:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:3447:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3447:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:3453:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3453:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:3453:52: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3453:52: note: Null pointer dereference
Rsubread/src/cell-counts.c:3453:94: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3453:94: note: Null pointer dereference
Rsubread/src/cell-counts.c:3456:7: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3456:7: note: Null pointer dereference
Rsubread/src/cell-counts.c:3457:73: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3457:73: note: Null pointer dereference
Rsubread/src/cell-counts.c:3457:100: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3457:100: note: Null pointer dereference
Rsubread/src/cell-counts.c:3458:61: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3458:61: note: Null pointer dereference
Rsubread/src/cell-counts.c:3458:102: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3458:102: note: Null pointer dereference
Rsubread/src/cell-counts.c:3458:151: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3458:151: note: Null pointer dereference
Rsubread/src/cell-counts.c:3459:20: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3459:20: note: Null pointer dereference
Rsubread/src/cell-counts.c:3462:75: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3459:19: note: Assuming condition is false
Rsubread/src/cell-counts.c:3462:75: note: Null pointer dereference
Rsubread/src/cell-counts.c:3462:102: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:3459:19: note: Assuming condition is false
Rsubread/src/cell-counts.c:3462:102: note: Null pointer dereference
Rsubread/src/cell-counts.c:3996:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:3995:20: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3995:20: note: Assignment 'fp=fopen(tmp_fname,"rb")', assigned value is 0
Rsubread/src/cell-counts.c:3996:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:3997:33: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:3995:20: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3995:20: note: Assignment 'fp=fopen(tmp_fname,"rb")', assigned value is 0
Rsubread/src/cell-counts.c:3997:33: note: Null pointer dereference
Rsubread/src/cell-counts.c:3998:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:3995:20: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3995:20: note: Assignment 'fp=fopen(tmp_fname,"rb")', assigned value is 0
Rsubread/src/cell-counts.c:3998:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:4000:38: warning: If memory allocation fails, then there is a possible null pointer dereference: batch_content [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:3999:49: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3999:49: note: Assignment 'batch_content=malloc(batch_fsize)', assigned value is 0
Rsubread/src/cell-counts.c:4000:38: note: Null pointer dereference
Rsubread/src/cell-counts.c:4000:69: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:3995:20: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3995:20: note: Assignment 'fp=fopen(tmp_fname,"rb")', assigned value is 0
Rsubread/src/cell-counts.c:4000:69: note: Null pointer dereference
Rsubread/src/cell-counts.c:4001:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:3995:20: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:3995:20: note: Assignment 'fp=fopen(tmp_fname,"rb")', assigned value is 0
Rsubread/src/cell-counts.c:4001:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:4052:4: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4052:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:4053:37: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4053:37: note: Null pointer dereference
Rsubread/src/cell-counts.c:4059:55: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4059:55: note: Null pointer dereference
Rsubread/src/cell-counts.c:4067:4: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4067:4: note: Null pointer dereference
Rsubread/src/cell-counts.c:4073:18: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4073:18: note: Null pointer dereference
Rsubread/src/cell-counts.c:4074:47: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4074:47: note: Null pointer dereference
Rsubread/src/cell-counts.c:4078:18: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4078:18: note: Null pointer dereference
Rsubread/src/cell-counts.c:4080:47: warning: If memory allocation fails, then there is a possible null pointer dereference: cell_gene_umi_list [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4050:43: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4050:43: note: Assignment 'cell_gene_umi_list=malloc(sizeof(void*)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4080:47: note: Null pointer dereference
Rsubread/src/cell-counts.c:4084:65: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4062:13: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4062:13: note: Assignment 'fp=fopen(tmp_fname,"wb")', assigned value is 0
Rsubread/src/cell-counts.c:4084:65: note: Null pointer dereference
Rsubread/src/cell-counts.c:4213:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp_mtx [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4212:24: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4212:24: note: Assignment 'ofp_mtx=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4213:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:4230:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp_mtx [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4212:24: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4212:24: note: Assignment 'ofp_mtx=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4230:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:4236:11: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp_genes [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4210:26: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4210:26: note: Assignment 'ofp_genes=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4236:11: note: Null pointer dereference
Rsubread/src/cell-counts.c:4242:11: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp_bcs [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4208:24: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4208:24: note: Assignment 'ofp_bcs=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4242:11: note: Null pointer dereference
Rsubread/src/cell-counts.c:4297:10: warning: If resource allocation fails, then there is a possible null pointer dereference: write_fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4296:25: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4296:25: note: Assignment 'write_fp=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4297:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:4308:9: warning: If resource allocation fails, then there is a possible null pointer dereference: write_fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4296:25: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4296:25: note: Assignment 'write_fp=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4308:9: note: Null pointer dereference
Rsubread/src/cell-counts.c:4329:9: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4321:19: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4321:19: note: Assignment 'fp=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4329:9: note: Null pointer dereference
Rsubread/src/cell-counts.c:4449:10: warning: If resource allocation fails, then there is a possible null pointer dereference: sample_tab_fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4446:30: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4446:30: note: Assignment 'sample_tab_fp=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4449:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:4469:11: warning: If resource allocation fails, then there is a possible null pointer dereference: sample_tab_fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4446:30: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4446:30: note: Assignment 'sample_tab_fp=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4469:11: note: Null pointer dereference
Rsubread/src/cell-counts.c:4501:9: warning: If resource allocation fails, then there is a possible null pointer dereference: sample_tab_fp [nullPointerOutOfResources]
Rsubread/src/cell-counts.c:4446:30: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4446:30: note: Assignment 'sample_tab_fp=fopen(ofname,"w")', assigned value is 0
Rsubread/src/cell-counts.c:4501:9: note: Null pointer dereference
Rsubread/src/cell-counts.c:4535:49: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4535:49: note: Null pointer dereference
Rsubread/src/cell-counts.c:4536:42: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4536:42: note: Null pointer dereference
Rsubread/src/cell-counts.c:4537:43: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4537:43: note: Null pointer dereference
Rsubread/src/cell-counts.c:4538:136: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4538:136: note: Null pointer dereference
Rsubread/src/cell-counts.c:4539:41: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4539:41: note: Null pointer dereference
Rsubread/src/cell-counts.c:4548:10: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4548:10: note: Null pointer dereference
Rsubread/src/cell-counts.c:4552:34: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4552:34: note: Null pointer dereference
Rsubread/src/cell-counts.c:4553:18: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4879:39: note: Calling function 'cellCounts_run_counting', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4855:44: note: Calling function 'cellCounts_do_cellbc_batches', 1st argument 'cct_context' value is 0
Rsubread/src/cell-counts.c:4553:18: note: Null pointer dereference
Rsubread/src/cell-counts.c:4557:3: warning: If memory allocation fails, then there is a possible null pointer dereference: task_buffers [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4538:64: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4538:64: note: Assignment 'task_buffers=malloc(sizeof(struct scRNA_merge_batches_worker_task)*(1+compress_workers)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4557:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4558:3: warning: If memory allocation fails, then there is a possible null pointer dereference: task_buffers [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4538:64: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4538:64: note: Assignment 'task_buffers=malloc(sizeof(struct scRNA_merge_batches_worker_task)*(1+compress_workers)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4558:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4559:3: warning: If memory allocation fails, then there is a possible null pointer dereference: task_buffers [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4538:64: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4538:64: note: Assignment 'task_buffers=malloc(sizeof(struct scRNA_merge_batches_worker_task)*(1+compress_workers)*cct_context->sample_sheet_table->numOfElements)', assigned value is 0
Rsubread/src/cell-counts.c:4559:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4567:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vpp [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4566:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4566:23: note: Assignment 'vpp=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/cell-counts.c:4567:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4568:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vpp [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4566:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4566:23: note: Assignment 'vpp=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/cell-counts.c:4568:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4569:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vpp [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4566:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4566:23: note: Assignment 'vpp=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/cell-counts.c:4569:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4616:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vpp [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4615:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4615:23: note: Assignment 'vpp=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:4616:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4617:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vpp [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4615:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4615:23: note: Assignment 'vpp=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:4617:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4618:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vpp [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4615:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4615:23: note: Assignment 'vpp=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:4618:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4619:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vpp [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4615:23: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4615:23: note: Assignment 'vpp=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/cell-counts.c:4619:3: note: Null pointer dereference
Rsubread/src/cell-counts.c:4873:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4873:2: note: Null pointer dereference
Rsubread/src/cell-counts.c:4881:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
Rsubread/src/cell-counts.c:4881:5: note: Null pointer dereference
Rsubread/src/cell-counts.c:738:30: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/cell-counts.c:722:25: note: Assuming allocation function fails
Rsubread/src/cell-counts.c:722:25: note: Assignment 'outbuff=malloc(outcapa)', assigned value is 0
Rsubread/src/cell-counts.c:725:13: note: Assuming condition is false
Rsubread/src/cell-counts.c:738:30: note: Null pointer addition
Rsubread/src/cell-counts.c:944:10: style: Local variable 'tmp_chro_name' shadows outer variable [shadowVariable]
Rsubread/src/cell-counts.c:917:7: note: Shadowed declaration
Rsubread/src/cell-counts.c:944:10: note: Shadow variable
Rsubread/src/cell-counts.c:1750:13: style: Local variable 'xx2' shadows outer variable [shadowVariable]
Rsubread/src/cell-counts.c:1724:7: note: Shadowed declaration
Rsubread/src/cell-counts.c:1750:13: note: Shadow variable
Rsubread/src/cell-counts.c:2515:7: style: Local variable 'first_half_matched' shadows outer variable [shadowVariable]
Rsubread/src/cell-counts.c:2484:17: note: Shadowed declaration
Rsubread/src/cell-counts.c:2515:7: note: Shadow variable
Rsubread/src/cell-counts.c:2516:7: style: Local variable 'second_half_matched' shadows outer variable [shadowVariable]
Rsubread/src/cell-counts.c:2484:60: note: Shadowed declaration
Rsubread/src/cell-counts.c:2516:7: note: Shadow variable
Rsubread/src/cell-counts.c:4173:8: style: Local variable 'block_number_this' shadows outer variable [shadowVariable]
Rsubread/src/cell-counts.c:4159:7: note: Shadowed declaration
Rsubread/src/cell-counts.c:4173:8: note: Shadow variable
Rsubread/src/cell-counts.c:4729:8: style: Local variable 'binlen' shadows outer variable [shadowVariable]
Rsubread/src/cell-counts.c:4692:22: note: Shadowed declaration
Rsubread/src/cell-counts.c:4729:8: note: Shadow variable
Rsubread/src/cell-counts.c:4730:13: style: Local variable 'genes' shadows outer variable [shadowVariable]
Rsubread/src/cell-counts.c:4693:12: note: Shadowed declaration
Rsubread/src/cell-counts.c:4730:13: note: Shadow variable
Rsubread/src/cell-counts.c:1387:61: style: Argument '1||(cct_context->input_mode==3)' to function cellCounts_init_lock is always 1. It does not matter what value 'cct_context->input_mode' has. [knownArgument]
Rsubread/src/cell-counts.c:239:36: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:279:10: style: Variable 'bc' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:319:36: style: Parameter 'read_bin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:433:31: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:441:9: style: Variable 'current_keys' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:617:9: style: Variable 'DBPZ_var_candidates' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:618:9: style: Variable 'DBPZ_var_topdiff' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:792:10: style: Variable 'sample_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:882:74: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1074:13: style: Variable 'ret_start' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:1178:30: style: Variable 'chro_stub' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:1312:12: style: Variable 't1chro' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:1313:32: style: Variable 'chro_stub' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:1472:53: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1478:53: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1546:69: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1561:102: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1586:103: style: Parameter 'chro_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1595:11: style: Variable 'anno_chro_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:1786:54: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1786:102: style: Parameter 'read_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1786:194: style: Parameter 'qual_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1786:212: style: Parameter 'chro_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1850:58: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1850:142: style: Parameter 'umi_barcode' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:1850:162: style: Parameter 'readbin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2133:64: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2189:58: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2192:9: style: Variable 'r1_cigar' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2211:101: style: Parameter 'readbin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2316:56: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2332:121: style: Parameter 'read_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2368:54: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2368:89: style: Parameter 'read_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2368:107: style: Parameter 'read_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2368:125: style: Parameter 'qual_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2446:37: style: Parameter 'read_bin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2528:54: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2528:89: style: Parameter 'read_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2528:143: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2651:30: style: Variable 'thread_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2652:8: style: Variable 'sorting_index' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2739:9: style: Variable 'keyc' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2749:8: style: Variable 'Xptrs' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2750:8: style: Variable 'trying_subread_no' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2801:66: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2821:18: style: Variable 'index_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2830:26: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2900:77: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:2932:18: style: Variable 'index_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:2948:26: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3032:59: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:3032:139: style: Parameter 'read_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:3057:70: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:3282:47: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:3527:43: style: Parameter 'u1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:3527:54: style: Parameter 'u2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:3540:24: style: Variable 'cct_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3549:33: style: Variable 'str2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3662:24: style: Variable 'cct_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3671:31: style: Variable 'str1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3678:33: style: Variable 'strold' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3686:32: style: Variable 'str0' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3700:24: style: Variable 'cct_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3742:29: style: Variable 'L' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3742:42: style: Variable 'R' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3744:24: style: Variable 'cct_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3772:65: style: Parameter 'val' can be declared as pointer to const. However it seems that 'cellCounts_do_one_batch_tab_to_struct_list' is a callback function, if 'val' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4058:39: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:3772:65: note: Parameter 'val' can be declared as pointer to const
Rsubread/src/cell-counts.c:3793:48: style: Parameter 'vcell_gene' can be declared as pointer to const. However it seems that 'cellCounts_do_one_batch_write_UMIs' is a callback function, if 'vcell_gene' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4085:56: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:3793:48: note: Parameter 'vcell_gene' can be declared as pointer to const
Rsubread/src/cell-counts.c:3793:67: style: Parameter 'vumis' can be declared as pointer to const. However it seems that 'cellCounts_do_one_batch_write_UMIs' is a callback function, if 'vumis' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4085:56: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:3793:67: note: Parameter 'vumis' can be declared as pointer to const
Rsubread/src/cell-counts.c:3803:24: style: Variable 'cct_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3862:10: style: Variable 'tagstr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4150:55: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:4183:57: style: Parameter 'ky' can be declared as pointer to const. However it seems that 'cellCounts_merged_write_sparse_unique_genes' is a callback function, if 'ky' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4490:52: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4183:57: note: Parameter 'ky' can be declared as pointer to const
Rsubread/src/cell-counts.c:4185:14: style: Variable 'used_cellnoP1_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4193:9: style: Variable 'geneno1B_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4235:9: style: Variable 'gene_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4241:10: style: Variable 'cellbc_seq' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4247:15: style: Variable 'geneno1B_to_UMIs' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4263:57: style: Parameter 'GeneNo1B' can be declared as pointer to const. However it seems that 'cellCounts_merged_45K_to_90K_sum_SUM_Level2' is a callback function, if 'GeneNo1B' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4274:43: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4263:57: note: Parameter 'GeneNo1B' can be declared as pointer to const
Rsubread/src/cell-counts.c:4268:50: style: Parameter 'keyCellNoP1' can be declared as pointer to const. However it seems that 'cellCounts_merged_45K_to_90K_sum_SUM' is a callback function, if 'keyCellNoP1' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4292:46: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4268:50: note: Parameter 'keyCellNoP1' can be declared as pointer to const
Rsubread/src/cell-counts.c:4270:14: style: Variable 'bcid_look_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4277:50: style: Parameter 'kyGeneID' can be declared as pointer to const. However it seems that 'cellCounts_merged_45K_to_90K_sum_WRT' is a callback function, if 'kyGeneID' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4305:43: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4277:50: note: Parameter 'kyGeneID' can be declared as pointer to const
Rsubread/src/cell-counts.c:4277:67: style: Parameter 'valUMIs' can be declared as pointer to const. However it seems that 'cellCounts_merged_45K_to_90K_sum_WRT' is a callback function, if 'valUMIs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4305:43: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4277:67: note: Parameter 'valUMIs' can be declared as pointer to const
Rsubread/src/cell-counts.c:4282:18: style: Variable 'gene_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4311:55: style: Parameter 'k' can be declared as pointer to const. However it seems that 'cellCounts_merged_write_nozero_geneids_WRT' is a callback function, if 'k' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4328:31: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4311:55: note: Parameter 'k' can be declared as pointer to const
Rsubread/src/cell-counts.c:4314:17: style: Variable 'gene_symbol' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4332:76: style: Parameter 'val' can be declared as pointer to const. However it seems that 'cellCounts_merged_to_tables_write_build_UMIcount_in' is a callback function, if 'val' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4342:43: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4332:76: note: Parameter 'val' can be declared as pointer to const
Rsubread/src/cell-counts.c:4336:63: style: Parameter 'ky' can be declared as pointer to const. However it seems that 'cellCounts_merged_to_tables_write_build_UMIcounts' is a callback function, if 'ky' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/cell-counts.c:4457:52: note: You might need to cast the function pointer here
Rsubread/src/cell-counts.c:4336:63: note: Parameter 'ky' can be declared as pointer to const
Rsubread/src/cell-counts.c:4354:10: style: Variable 'this_bc_pnt' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4389:64: style: Parameter 'cct_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/cell-counts.c:4400:11: style: Variable 'cellbc_p1_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4412:12: style: Variable 'cellbc_p1_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4465:10: style: Variable 'this_sample_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:4474:24: style: Variable 'feature1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/cell-counts.c:3551:6: portability: 'HashTableGet(cellBCp0_genep0_P1_to_UMIs,NULL+1+(((1LLU*str1->cellbc)<<32)|(str1->gene_no)))' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:3688:45: portability: 'HashTableGet(cellBCp0_genep0_P1_to_UMIs,NULL+1+(((1LLU*str0->cellbc)<<32)|(str0->gene_no)))' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:3795:13: portability: 'vcell_gene' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:4265:52: portability: 'vUMIs' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:4373:68: portability: 'this_bc_pnt_p1' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:4378:86: portability: 'ArrayListGet(sorted_bcno_p1,x1)' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:4403:72: portability: 'ArrayListGet(sorted_idx,x1)' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:4435:49: portability: 'last_ptr' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:4480:105: portability: 'all_barcode_index_list->elementList[xk1]' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/cell-counts.c:1622:6: warning: Uninitialized variable: search_start [uninitvar]
Rsubread/src/cell-counts.c:1616:34: note: Assuming condition is false
Rsubread/src/cell-counts.c:1622:6: note: Uninitialized variable: search_start
Rsubread/src/cell-counts.c:1821:35: warning: Uninitialized variable: cigar_opts [uninitvar]
Rsubread/src/cell-counts.c:1801:5: note: Assuming condition is false
Rsubread/src/cell-counts.c:1821:35: note: Uninitialized variable: cigar_opts
Rsubread/src/cell-counts.c:68:15: style: struct member 'voting_location_t::selected_position' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:69:8: style: struct member 'voting_location_t::result_flags' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:70:8: style: struct member 'voting_location_t::read_length' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:72:21: style: struct member 'voting_location_t::selected_votes' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:73:21: style: struct member 'voting_location_t::used_subreads_in_vote' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:74:7: style: struct member 'voting_location_t::indels_in_confident_coverage' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:75:7: style: struct member 'voting_location_t::is_fully_covered' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:76:21: style: struct member 'voting_location_t::selected_indel_record' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:77:17: style: struct member 'voting_location_t::confident_coverage_start' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:78:17: style: struct member 'voting_location_t::confident_coverage_end' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:230:6: style: struct member 'cellcounts_final_thread_t::thread_no' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1485:6: style: struct member 'AT_context_t::thread_id' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1486:6: style: struct member 'AT_context_t::block_start' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1487:6: style: struct member 'AT_context_t::block_end' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1488:14: style: struct member 'AT_context_t::result_tab' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1489:8: style: struct member 'AT_context_t::small_side_ordered_event_ids' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1489:40: style: struct member 'AT_context_t::large_side_ordered_event_ids' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1490:23: style: struct member 'AT_context_t::event_space' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:1491:24: style: struct member 'AT_context_t::cct_context' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:2185:15: style: struct member 'concatinating_events_record_t::thread_bodytable_number' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:2186:8: style: struct member 'concatinating_events_record_t::thread_no' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:2363:15: style: struct member 'scanning_events_record_t::scanning_positons' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:2364:15: style: struct member 'scanning_events_record_t::thread_bodytable_number' is never used. [unusedStructMember]
Rsubread/src/cell-counts.c:329:47: style: Variable 'removed_base_index' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:2144:6: style: Variable 'ret_values' is not assigned a value. [unassignedVariable]
Rsubread/src/cell-counts.c:2431:9: style: Variable 'toli' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4635:17: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4638:11: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4639:11: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4660:17: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4662:10: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4734:17: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4736:10: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4781:16: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/cell-counts.c:4784:9: style: Variable 'frret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-interface-aligner.c:658:68: style: Same expression on both sides of '-'. [duplicateExpression]
Rsubread/src/core-interface-subjunc.c:81:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/core-interface-subjunc.c:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/core-junction.c:136:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core-junction.c:596:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core-junction.c:1734:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core-junction.c:3201:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable read_pos_end [valueFlowBailoutIncompleteVar]
Rsubread/src/core-junction.c:3953:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core-junction.c:4394:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core-junction.c:5160:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core-indel.c:2643:21: warning: Either the condition 'inserted_length>200+350-1' is redundant or the array 'inserted_sequence[550]' is accessed at index 550, which is out of bounds. [arrayIndexOutOfBoundsCond]
Rsubread/src/core-indel.c:2640:22: note: Assuming that condition 'inserted_length>200+350-1' is not redundant
Rsubread/src/core-indel.c:2643:21: note: Array index out of bounds
Rsubread/src/core-indel.c:1867:26: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
Rsubread/src/core-indel.c:1874:25: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
Rsubread/src/core-indel.c:4688:22: style: Expression is always true because 'else if' condition is opposite to previous condition at line 4683. [multiCondition]
Rsubread/src/core-indel.c:4683:22: note: first condition
Rsubread/src/core-indel.c:4688:22: note: else if condition is opposite to first condition
Rsubread/src/core-indel.c:3751:5: warning: Identical condition '!tmp_fp', second condition is always false [identicalConditionAfterEarlyExit]
Rsubread/src/core-indel.c:3704:5: note: If condition '!tmp_fp' is true, the function will return/exit
Rsubread/src/core-indel.c:3751:5: note: Testing identical condition '!tmp_fp'
Rsubread/src/core-indel.c:589:10: style: Condition '0&&wrt_ptr==1' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:1205:12: style: Condition '1||newbody->event_small_side==625683723' is always true [knownConditionTrueFalse]
Rsubread/src/core-indel.c:1892:26: style: Condition 'first_correct_base<last_correct_base' is always true [knownConditionTrueFalse]
Rsubread/src/core-indel.c:1890:23: note: first_correct_base is assigned '(first_correct_base)<(last_correct_base)?(last_correct_base):(first_correct_base)' here.
Rsubread/src/core-indel.c:1892:26: note: Condition 'first_correct_base<last_correct_base' is always true
Rsubread/src/core-indel.c:1910:10: style: Condition '0&&FIXLENstrcmp("simulated.2467286",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:1941:98: style: Condition 'total_mismatch<=2' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:1941:22: note: Assuming that condition 'total_mismatch<=2' is not redundant
Rsubread/src/core-indel.c:1941:98: note: Condition 'total_mismatch<=2' is always false
Rsubread/src/core-indel.c:2063:18: style: Condition 'score>best_score' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:2059:21: note: best_score is assigned 'score' here.
Rsubread/src/core-indel.c:2063:18: note: Condition 'score>best_score' is always false
Rsubread/src/core-indel.c:4607:7: style: Condition '0&&strcmp(read_name,"MISEQ:13:000000000-A1H1M:1:1112:12194:5511")==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:4627:8: style: Condition '0&&(i>=read_len+expected_offset||j>=read_len)' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:4631:8: style: Condition '0&&(i>=read_len+expected_offset||j>=read_len)' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:4637:10: style: Condition '0&&strcmp(read_name,"MISEQ:13:000000000-A1H1M:1:1112:12194:5511")==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:4694:9: style: Condition '0&&strcmp(read_name,"MISEQ:13:000000000-A1H1M:1:1112:12194:5511")==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:4697:8: style: Condition '0&&strcmp(read_name,"MISEQ:13:000000000-A1H1M:1:1112:12194:5511")==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:4711:7: style: Condition '0&&strcmp(read_name,"MISEQ:13:000000000-A1H1M:1:1112:12194:5511")==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:4771:7: style: Condition '0&&strcmp(read_name,"MISEQ:13:000000000-A1H1M:1:1112:12194:5511")==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-indel.c:2314:20: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-indel.c:4146:9: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-indel.c:4146:9: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-indel.c:4148:9: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-indel.c:4148:9: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-indel.c:185:35: error: Memory leak: cancelled_event_list [memleak]
Rsubread/src/core-indel.c:711:4: error: Memory leak: indel_thread_context [memleak]
Rsubread/src/core-indel.c:464:4: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:477:5: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:490:7: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:536:8: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:553:7: error: Common realloc mistake: 'to_be_removed_ids' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:883:3: error: Common realloc mistake: 'records' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:1030:6: error: Common realloc mistake: 'records' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:1039:4: error: Common realloc mistake: 'records' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:1068:7: error: Common realloc mistake: 'merge_target' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/core-indel.c:3751:14: error: Memory leak: block_context.voting_indexes [memleak]
Rsubread/src/core-indel.c:3751:14: error: Memory leak: block_context.start_keys [memleak]
Rsubread/src/core-indel.c:3751:14: error: Memory leak: block_context.start_offsets [memleak]
Rsubread/src/core-indel.c:3751:14: error: Memory leak: block_context.read_no_counter [memleak]
Rsubread/src/core-indel.c:3751:14: error: Memory leak: block_context.read_rectify_space [memleak]
Rsubread/src/core-indel.c:3751:14: error: Memory leak: block_context.final_alleles [memleak]
Rsubread/src/core-indel.c:83:4: warning: If memory allocation fails, then there is a possible null pointer dereference: merge_tmp [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:57:26: note: Assuming allocation function fails
Rsubread/src/core-indel.c:57:26: note: Assignment 'merge_tmp=malloc(sizeof(int)*(items+items2))', assigned value is 0
Rsubread/src/core-indel.c:83:4: note: Null pointer dereference
Rsubread/src/core-indel.c:85:4: warning: If memory allocation fails, then there is a possible null pointer dereference: merge_tmp [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:57:26: note: Assuming allocation function fails
Rsubread/src/core-indel.c:57:26: note: Assignment 'merge_tmp=malloc(sizeof(int)*(items+items2))', assigned value is 0
Rsubread/src/core-indel.c:85:4: note: Null pointer dereference
Rsubread/src/core-indel.c:89:32: warning: If memory allocation fails, then there is a possible null pointer dereference: merge_tmp [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:57:26: note: Assuming allocation function fails
Rsubread/src/core-indel.c:57:26: note: Assignment 'merge_tmp=malloc(sizeof(int)*(items+items2))', assigned value is 0
Rsubread/src/core-indel.c:89:32: note: Null pointer dereference
Rsubread/src/core-indel.c:282:3: warning: If memory allocation fails, then there is a possible null pointer dereference: small_side_ordered_event_ids [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:278:39: note: Assuming allocation function fails
Rsubread/src/core-indel.c:278:39: note: Assignment 'small_side_ordered_event_ids=malloc(sizeof(int)*indel_context->total_events)', assigned value is 0
Rsubread/src/core-indel.c:282:3: note: Null pointer dereference
Rsubread/src/core-indel.c:283:3: warning: If memory allocation fails, then there is a possible null pointer dereference: large_side_ordered_event_ids [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:279:39: note: Assuming allocation function fails
Rsubread/src/core-indel.c:279:39: note: Assignment 'large_side_ordered_event_ids=malloc(sizeof(int)*indel_context->total_events)', assigned value is 0
Rsubread/src/core-indel.c:283:3: note: Null pointer dereference
Rsubread/src/core-indel.c:629:2: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:629:2: note: Null pointer dereference
Rsubread/src/core-indel.c:633:2: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:633:2: note: Null pointer dereference
Rsubread/src/core-indel.c:634:2: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:634:2: note: Null pointer dereference
Rsubread/src/core-indel.c:638:2: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:638:2: note: Null pointer dereference
Rsubread/src/core-indel.c:662:3: warning: If memory allocation fails, then there is a possible null pointer dereference: fns [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:661:22: note: Assuming allocation function fails
Rsubread/src/core-indel.c:661:22: note: Assignment 'fns=malloc(200)', assigned value is 0
Rsubread/src/core-indel.c:662:3: note: Null pointer dereference
Rsubread/src/core-indel.c:664:28: warning: If memory allocation fails, then there is a possible null pointer dereference: fns [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:661:22: note: Assuming allocation function fails
Rsubread/src/core-indel.c:661:22: note: Assignment 'fns=malloc(200)', assigned value is 0
Rsubread/src/core-indel.c:664:28: note: Null pointer dereference
Rsubread/src/core-indel.c:678:2: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:678:2: note: Null pointer dereference
Rsubread/src/core-indel.c:679:2: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:679:2: note: Null pointer dereference
Rsubread/src/core-indel.c:683:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:683:3: note: Null pointer dereference
Rsubread/src/core-indel.c:684:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:684:3: note: Null pointer dereference
Rsubread/src/core-indel.c:688:21: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:623:60: note: Assuming allocation function fails
Rsubread/src/core-indel.c:623:36: note: Assignment 'indel_context=(struct indel_context_t*)malloc(sizeof(struct indel_context_t))', assigned value is 0
Rsubread/src/core-indel.c:688:21: note: Null pointer dereference
Rsubread/src/core-indel.c:699:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:699:3: note: Null pointer dereference
Rsubread/src/core-indel.c:700:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:700:3: note: Null pointer dereference
Rsubread/src/core-indel.c:701:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:701:3: note: Null pointer dereference
Rsubread/src/core-indel.c:702:37: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:702:37: note: Null pointer dereference
Rsubread/src/core-indel.c:703:28: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:703:28: note: Null pointer dereference
Rsubread/src/core-indel.c:705:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:705:3: note: Null pointer dereference
Rsubread/src/core-indel.c:706:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:706:3: note: Null pointer dereference
Rsubread/src/core-indel.c:707:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:707:3: note: Null pointer dereference
Rsubread/src/core-indel.c:707:83: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:707:83: note: Null pointer dereference
Rsubread/src/core-indel.c:708:7: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:708:7: note: Null pointer dereference
Rsubread/src/core-indel.c:726:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:726:3: note: Null pointer dereference
Rsubread/src/core-indel.c:727:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:727:3: note: Null pointer dereference
Rsubread/src/core-indel.c:728:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:728:3: note: Null pointer dereference
Rsubread/src/core-indel.c:729:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:729:3: note: Null pointer dereference
Rsubread/src/core-indel.c:730:3: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:730:3: note: Null pointer dereference
Rsubread/src/core-indel.c:731:10: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:731:10: note: Null pointer dereference
Rsubread/src/core-indel.c:733:10: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:733:10: note: Null pointer dereference
Rsubread/src/core-indel.c:734:10: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
Rsubread/src/core-indel.c:734:10: note: Null pointer dereference
Rsubread/src/core-indel.c:812:26: warning: If memory allocation fails, then there is a possible null pointer dereference: merged_records [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:804:52: note: Assuming allocation function fails
Rsubread/src/core-indel.c:804:52: note: Assignment 'merged_records=malloc(sizeof(struct scanning_events_record_t)*(items+items2))', assigned value is 0
Rsubread/src/core-indel.c:812:26: note: Null pointer dereference
Rsubread/src/core-indel.c:894:36: warning: If memory allocation fails, then there is a possible null pointer dereference: records [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:879:45: note: Assuming allocation function fails
Rsubread/src/core-indel.c:879:45: note: Assignment 'records=malloc(sizeof(struct scanning_events_record_t)*current_record_size)', assigned value is 0
Rsubread/src/core-indel.c:881:19: note: Assuming condition is false
Rsubread/src/core-indel.c:894:36: note: Null pointer dereference
Rsubread/src/core-indel.c:986:26: warning: If memory allocation fails, then there is a possible null pointer dereference: merged_records [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:978:57: note: Assuming allocation function fails
Rsubread/src/core-indel.c:978:57: note: Assignment 'merged_records=malloc(sizeof(struct concatinating_events_record_t)*(items+items2))', assigned value is 0
Rsubread/src/core-indel.c:986:26: note: Null pointer dereference
Rsubread/src/core-indel.c:1270:11: warning: If memory allocation fails, then there is a possible null pointer dereference: old_features2 [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1269:32: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1269:32: note: Assignment 'old_features2=malloc(sizeof(int)*(old_features[0]+1))', assigned value is 0
Rsubread/src/core-indel.c:1270:11: note: Null pointer dereference
Rsubread/src/core-indel.c:1271:4: warning: If memory allocation fails, then there is a possible null pointer dereference: old_features2 [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1269:32: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1269:32: note: Assignment 'old_features2=malloc(sizeof(int)*(old_features[0]+1))', assigned value is 0
Rsubread/src/core-indel.c:1271:4: note: Null pointer dereference
Rsubread/src/core-indel.c:1276:19: warning: If memory allocation fails, then there is a possible null pointer dereference: old_features [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1269:32: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1269:32: note: Assignment 'old_features2=malloc(sizeof(int)*(old_features[0]+1))', assigned value is 0
Rsubread/src/core-indel.c:1274:19: note: Assignment 'old_features=old_features2', assigned value is 0
Rsubread/src/core-indel.c:1276:19: note: Null pointer dereference
Rsubread/src/core-indel.c:1297:3: warning: If memory allocation fails, then there is a possible null pointer dereference: old_features [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1296:24: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1296:24: note: Assignment 'old_features=malloc((init_space_sort+1)*sizeof(int))', assigned value is 0
Rsubread/src/core-indel.c:1297:3: note: Null pointer dereference
Rsubread/src/core-indel.c:1299:10: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_sort_key [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1298:30: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1298:30: note: Assignment 'mm_sort_key=malloc(strlen(sort_key)+1)', assigned value is 0
Rsubread/src/core-indel.c:1299:10: note: Null pointer dereference
Rsubread/src/core-indel.c:1401:4: warning: If memory allocation fails, then there is a possible null pointer dereference: id_list [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1400:20: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1400:20: note: Assignment 'id_list=malloc(sizeof(unsigned int)*(1+9))', assigned value is 0
Rsubread/src/core-indel.c:1401:4: note: Null pointer dereference
Rsubread/src/core-indel.c:1402:4: warning: If memory allocation fails, then there is a possible null pointer dereference: id_list [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1400:20: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1400:20: note: Assignment 'id_list=malloc(sizeof(unsigned int)*(1+9))', assigned value is 0
Rsubread/src/core-indel.c:1402:4: note: Null pointer dereference
Rsubread/src/core-indel.c:1406:18: warning: If memory allocation fails, then there is a possible null pointer dereference: id_list [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1400:20: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1400:20: note: Assignment 'id_list=malloc(sizeof(unsigned int)*(1+9))', assigned value is 0
Rsubread/src/core-indel.c:1406:18: note: Null pointer dereference
Rsubread/src/core-indel.c:1407:7: warning: If memory allocation fails, then there is a possible null pointer dereference: id_list [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:1400:20: note: Assuming allocation function fails
Rsubread/src/core-indel.c:1400:20: note: Assignment 'id_list=malloc(sizeof(unsigned int)*(1+9))', assigned value is 0
Rsubread/src/core-indel.c:1407:7: note: Null pointer dereference
Rsubread/src/core-indel.c:3745:9: warning: If memory allocation fails, then there is a possible null pointer dereference: window_center_read_no [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:3709:64: note: Assuming allocation function fails
Rsubread/src/core-indel.c:3709:41: note: Assignment 'window_center_read_no=(unsigned int*)malloc(sizeof(unsigned int)*total_window_number*global_context->config.reassembly_start_read_number)', assigned value is 0
Rsubread/src/core-indel.c:3745:9: note: Null pointer dereference
Rsubread/src/core-indel.c:3746:9: warning: If memory allocation fails, then there is a possible null pointer dereference: window_center_read_qual [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:3711:66: note: Assuming allocation function fails
Rsubread/src/core-indel.c:3711:43: note: Assignment 'window_center_read_qual=(unsigned int*)malloc(sizeof(unsigned int)*total_window_number*global_context->config.reassembly_start_read_number)', assigned value is 0
Rsubread/src/core-indel.c:3746:9: note: Null pointer dereference
Rsubread/src/core-indel.c:3747:9: warning: If memory allocation fails, then there is a possible null pointer dereference: window_center_read_masks [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:3712:67: note: Assuming allocation function fails
Rsubread/src/core-indel.c:3712:44: note: Assignment 'window_center_read_masks=(unsigned int*)malloc(sizeof(unsigned int)*total_window_number)', assigned value is 0
Rsubread/src/core-indel.c:3747:9: note: Null pointer dereference
Rsubread/src/core-indel.c:3748:9: warning: If memory allocation fails, then there is a possible null pointer dereference: window_base_number [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:3710:61: note: Assuming allocation function fails
Rsubread/src/core-indel.c:3710:38: note: Assignment 'window_base_number=(unsigned int*)malloc(sizeof(unsigned int)*total_window_number)', assigned value is 0
Rsubread/src/core-indel.c:3748:9: note: Null pointer dereference
Rsubread/src/core-indel.c:4210:2: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4210:2: note: Null pointer dereference
Rsubread/src/core-indel.c:4211:2: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4211:2: note: Null pointer dereference
Rsubread/src/core-indel.c:4212:2: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4212:2: note: Null pointer dereference
Rsubread/src/core-indel.c:4214:9: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4214:9: note: Null pointer dereference
Rsubread/src/core-indel.c:4215:9: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4215:9: note: Null pointer dereference
Rsubread/src/core-indel.c:4217:2: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4217:2: note: Null pointer dereference
Rsubread/src/core-indel.c:4220:3: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4220:3: note: Null pointer dereference
Rsubread/src/core-indel.c:4221:3: warning: If memory allocation fails, then there is a possible null pointer dereference: block_context [nullPointerOutOfMemory]
Rsubread/src/core-indel.c:4209:82: note: Assuming allocation function fails
Rsubread/src/core-indel.c:4209:47: note: Assignment 'block_context=(struct reassembly_block_context_t*)malloc(sizeof(struct reassembly_block_context_t))', assigned value is 0
Rsubread/src/core-indel.c:4221:3: note: Null pointer dereference
Rsubread/src/core-indel.c:3077:72: style: Same expression on both sides of '-'. [duplicateExpression]
Rsubread/src/core-indel.c:2933:33: note: 'WINDOW_SEARCH_TREE_WIDTH' is assigned value '1' here.
Rsubread/src/core-indel.c:3077:72: note: Same expression on both sides of '-'.
Rsubread/src/core-indel.c:3124:44: style: Same expression on both sides of '-'. [duplicateExpression]
Rsubread/src/core-indel.c:2933:33: note: 'WINDOW_SEARCH_TREE_WIDTH' is assigned value '1' here.
Rsubread/src/core-indel.c:3124:44: note: Same expression on both sides of '-'.
Rsubread/src/core-indel.c:540:86: style: Unsigned expression 'tested_neighbour->event_large_side-tested_neighbour->event_small_side+tested_neighbour->indel_at_junction-event_body->event_large_side+event_body->event_small_side-event_body->indel_at_junction' can't be negative so it is unnecessary to test it. [unsignedPositive]
Rsubread/src/core-indel.c:2233:50: style:inconclusive: Function 'write_indel_final_results' argument 1 names different: declaration 'context' definition 'global_context'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:169:50: note: Function 'write_indel_final_results' argument 1 names different: declaration 'context' definition 'global_context'.
Rsubread/src/core-indel.c:2233:50: note: Function 'write_indel_final_results' argument 1 names different: declaration 'context' definition 'global_context'.
Rsubread/src/core-indel.c:2334:45: style:inconclusive: Function 'destroy_indel_module' argument 1 names different: declaration 'context' definition 'global_context'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:163:45: note: Function 'destroy_indel_module' argument 1 names different: declaration 'context' definition 'global_context'.
Rsubread/src/core-indel.c:2334:45: note: Function 'destroy_indel_module' argument 1 names different: declaration 'context' definition 'global_context'.
Rsubread/src/core-indel.c:2465:122: style:inconclusive: Function 'build_local_reassembly' argument 4 names different: declaration 'read_name_1' definition 'read_name'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:122: note: Function 'build_local_reassembly' argument 4 names different: declaration 'read_name_1' definition 'read_name'.
Rsubread/src/core-indel.c:2465:122: note: Function 'build_local_reassembly' argument 4 names different: declaration 'read_name_1' definition 'read_name'.
Rsubread/src/core-indel.c:2465:141: style:inconclusive: Function 'build_local_reassembly' argument 5 names different: declaration 'read_text_1' definition 'read_text'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:143: note: Function 'build_local_reassembly' argument 5 names different: declaration 'read_text_1' definition 'read_text'.
Rsubread/src/core-indel.c:2465:141: note: Function 'build_local_reassembly' argument 5 names different: declaration 'read_text_1' definition 'read_text'.
Rsubread/src/core-indel.c:2465:159: style:inconclusive: Function 'build_local_reassembly' argument 6 names different: declaration 'qual_text_1' definition 'qual_text'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:163: note: Function 'build_local_reassembly' argument 6 names different: declaration 'qual_text_1' definition 'qual_text'.
Rsubread/src/core-indel.c:2465:159: note: Function 'build_local_reassembly' argument 6 names different: declaration 'qual_text_1' definition 'qual_text'.
Rsubread/src/core-indel.c:2465:175: style:inconclusive: Function 'build_local_reassembly' argument 7 names different: declaration 'read_len_1' definition 'read_len'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:181: note: Function 'build_local_reassembly' argument 7 names different: declaration 'read_len_1' definition 'read_len'.
Rsubread/src/core-indel.c:2465:175: note: Function 'build_local_reassembly' argument 7 names different: declaration 'read_len_1' definition 'read_len'.
Rsubread/src/core-indel.c:2465:190: style:inconclusive: Function 'build_local_reassembly' argument 8 names different: declaration 'read_len_2' definition 'mate_read_len'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:197: note: Function 'build_local_reassembly' argument 8 names different: declaration 'read_len_2' definition 'mate_read_len'.
Rsubread/src/core-indel.c:2465:190: note: Function 'build_local_reassembly' argument 8 names different: declaration 'read_len_2' definition 'mate_read_len'.
Rsubread/src/core-indel.c:2465:248: style:inconclusive: Function 'build_local_reassembly' argument 11 names different: declaration 'is_paired_unmapped' definition 'use_mate_pos'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:251: note: Function 'build_local_reassembly' argument 11 names different: declaration 'is_paired_unmapped' definition 'use_mate_pos'.
Rsubread/src/core-indel.c:2465:248: note: Function 'build_local_reassembly' argument 11 names different: declaration 'is_paired_unmapped' definition 'use_mate_pos'.
Rsubread/src/core-indel.c:2465:280: style:inconclusive: Function 'build_local_reassembly' argument 12 names different: declaration 'current_res' definition 'current_result'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:290: note: Function 'build_local_reassembly' argument 12 names different: declaration 'current_res' definition 'current_result'.
Rsubread/src/core-indel.c:2465:280: note: Function 'build_local_reassembly' argument 12 names different: declaration 'current_res' definition 'current_result'.
Rsubread/src/core-indel.c:2465:314: style:inconclusive: Function 'build_local_reassembly' argument 13 names different: declaration 'mate_res' definition 'mate_result'. [funcArgNamesDifferent]
Rsubread/src/core-indel.h:176:322: note: Function 'build_local_reassembly' argument 13 names different: declaration 'mate_res' definition 'mate_result'.
Rsubread/src/core-indel.c:2465:314: note: Function 'build_local_reassembly' argument 13 names different: declaration 'mate_res' definition 'mate_result'.
Rsubread/src/core-indel.c:1956:30: style: Local variable 'current_value_index' shadows outer variable [shadowVariable]
Rsubread/src/core-indel.c:1863:23: note: Shadowed declaration
Rsubread/src/core-indel.c:1956:30: note: Shadow variable
Rsubread/src/core-indel.c:2124:9: style: Local variable 'j' shadows outer variable [shadowVariable]
Rsubread/src/core-indel.c:1833:8: note: Shadowed declaration
Rsubread/src/core-indel.c:2124:9: note: Shadow variable
Rsubread/src/core-indel.c:3095:14: style: Local variable 'next_read_pos' shadows outer variable [shadowVariable]
Rsubread/src/core-indel.c:2976:9: note: Shadowed declaration
Rsubread/src/core-indel.c:3095:14: note: Shadow variable
Rsubread/src/core-indel.c:46:25: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:46:44: style: Parameter 'w' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:68:25: style: Variable 'levent' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:69:25: style: Variable 'revent' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:109:23: style: Variable 'revent' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:110:23: style: Variable 'levent' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:129:8: style: Variable 'event_id_list' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:135:61: style: Parameter 'event_ids' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:184:20: style: Variable 'indel_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:197:23: style: Variable 'current_result' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:219:27: style: Variable 'event_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:233:27: style: Variable 'event_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:261:36: style: Parameter 'ky' can be declared as pointer to const. However it seems that 'anti_support_add_count' is a callback function, if 'ky' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/core-indel.c:322:54: note: You might need to cast the function pointer here
Rsubread/src/core-indel.c:261:36: note: Parameter 'ky' can be declared as pointer to const
Rsubread/src/core-indel.c:261:47: style: Parameter 'va' can be declared as pointer to const. However it seems that 'anti_support_add_count' is a callback function, if 'va' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/core-indel.c:322:54: note: You might need to cast the function pointer here
Rsubread/src/core-indel.c:261:47: note: Parameter 'va' can be declared as pointer to const
Rsubread/src/core-indel.c:408:46: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:408:82: style: Parameter 'testee' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:408:110: style: Parameter 'neighbour' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:461:24: style: Variable 'event_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:491:28: style: Variable 'tested_neighbour' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:537:29: style: Variable 'tested_neighbour' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:560:29: style: Variable 'tested_neighbour' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:775:20: style: Variable 'indel_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:798:40: style: Parameter 'arr' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:882:24: style: Variable 'body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:899:30: style: Variable 'this_record' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:911:27: style: Variable 'body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:947:20: style: Variable 'indel_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1024:30: style: Variable 'indel_thread_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1027:27: style: Variable 'old_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1037:25: style: Variable 'old_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1052:24: style: Variable 'prev_env' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1166:9: style: Variable 'gene_chr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1167:8: style: Variable 'pos_strands' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1339:38: style: Parameter 'bitmap' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:1359:40: style: Parameter 'bitmap' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:1439:17: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:1464:107: style: Parameter 'binary_bases' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:1479:130: style: Parameter 'read_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2230:43: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2465:280: style: Parameter 'current_result' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2465:314: style: Parameter 'mate_result' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2510:43: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2510:141: style: Parameter 'read_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2565:87: style: Parameter 'block_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2565:138: style: Parameter 'de_brujin_graph' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2785:42: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:3089:16: style: Variable 'prev_read_txt' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-indel.c:3452:22: style: Parameter 'c1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:3452:33: style: Parameter 'c2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:3461:53: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:3481:112: style: Parameter 'block_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:4199:81: style: Parameter 'temp_file_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:4573:202: style: Parameter 'read_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-indel.c:2594:22: style: Variable 'max_move_reads' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-indel.c:2643:38: style: Variable 'inserted_sequence[inserted_length]' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core.c:876:57: debug: Function::addArguments found argument 'int' with varid 0. [varid0]
Rsubread/src/core.c:67:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/core.c:123:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RLIMIT_NOFILE [valueFlowBailoutIncompleteVar]
Rsubread/src/core.c:611:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/core.c:872:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
Rsubread/src/core.c:1542:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable event_entry_table [valueFlowBailoutIncompleteVar]
Rsubread/src/core.c:3713:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/core.c:3721:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LC_NUMERIC [valueFlowBailoutIncompleteVar]
Rsubread/src/core.c:3870:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/core-interface-subjunc.c:682:68: style: Same expression on both sides of '-'. [duplicateExpression]
Rsubread/src/detection-calls.c:144:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
Rsubread/src/detection-calls.c:453:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/detection-calls.c:117:6: error: Common realloc mistake: 'base_2bits' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/detection-calls.c:52:10: warning: If memory allocation fails, then there is a possible null pointer dereference: new_exon [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:45:31: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:45:31: note: Assignment 'new_exon=malloc(sizeof(struct DTCexon_t))', assigned value is 0
Rsubread/src/detection-calls.c:52:10: note: Null pointer dereference
Rsubread/src/detection-calls.c:53:10: warning: If memory allocation fails, then there is a possible null pointer dereference: new_exon [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:45:31: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:45:31: note: Assignment 'new_exon=malloc(sizeof(struct DTCexon_t))', assigned value is 0
Rsubread/src/detection-calls.c:53:10: note: Null pointer dereference
Rsubread/src/detection-calls.c:54:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_exon [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:45:31: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:45:31: note: Assignment 'new_exon=malloc(sizeof(struct DTCexon_t))', assigned value is 0
Rsubread/src/detection-calls.c:54:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:55:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_exon [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:45:31: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:45:31: note: Assignment 'new_exon=malloc(sizeof(struct DTCexon_t))', assigned value is 0
Rsubread/src/detection-calls.c:55:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:56:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_exon [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:45:31: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:45:31: note: Assignment 'new_exon=malloc(sizeof(struct DTCexon_t))', assigned value is 0
Rsubread/src/detection-calls.c:56:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:102:5: warning: If memory allocation fails, then there is a possible null pointer dereference: curr_chro_mem [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:99:26: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:99:26: note: Assignment 'curr_chro_mem=malloc(strlen(fl))', assigned value is 0
Rsubread/src/detection-calls.c:102:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:104:4: warning: If memory allocation fails, then there is a possible null pointer dereference: curr_chro_mem [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:99:26: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:99:26: note: Assignment 'curr_chro_mem=malloc(strlen(fl))', assigned value is 0
Rsubread/src/detection-calls.c:104:4: note: Null pointer dereference
Rsubread/src/detection-calls.c:299:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_gene_info [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:298:27: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:298:27: note: Assignment 'tmp_gene_info=malloc(sizeof(unsigned int)*3)', assigned value is 0
Rsubread/src/detection-calls.c:299:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:300:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_gene_info [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:298:27: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:298:27: note: Assignment 'tmp_gene_info=malloc(sizeof(unsigned int)*3)', assigned value is 0
Rsubread/src/detection-calls.c:300:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:301:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_gene_info [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:298:27: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:298:27: note: Assignment 'tmp_gene_info=malloc(sizeof(unsigned int)*3)', assigned value is 0
Rsubread/src/detection-calls.c:301:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:305:6: warning: If memory allocation fails, then there is a possible null pointer dereference: gc_total_2int [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:304:28: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:304:28: note: Assignment 'gc_total_2int=malloc(sizeof(int)*2)', assigned value is 0
Rsubread/src/detection-calls.c:305:6: note: Null pointer dereference
Rsubread/src/detection-calls.c:305:25: warning: If memory allocation fails, then there is a possible null pointer dereference: gc_total_2int [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:304:28: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:304:28: note: Assignment 'gc_total_2int=malloc(sizeof(int)*2)', assigned value is 0
Rsubread/src/detection-calls.c:305:25: note: Null pointer dereference
Rsubread/src/detection-calls.c:308:5: warning: If memory allocation fails, then there is a possible null pointer dereference: gc_total_2int [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:304:28: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:304:28: note: Assignment 'gc_total_2int=malloc(sizeof(int)*2)', assigned value is 0
Rsubread/src/detection-calls.c:308:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:342:6: warning: If memory allocation fails, then there is a possible null pointer dereference: new_ME [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:341:36: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:341:36: note: Assignment 'new_ME=malloc(sizeof(struct MergedExon_t))', assigned value is 0
Rsubread/src/detection-calls.c:342:6: note: Null pointer dereference
Rsubread/src/detection-calls.c:343:6: warning: If memory allocation fails, then there is a possible null pointer dereference: new_ME [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:341:36: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:341:36: note: Assignment 'new_ME=malloc(sizeof(struct MergedExon_t))', assigned value is 0
Rsubread/src/detection-calls.c:343:6: note: Null pointer dereference
Rsubread/src/detection-calls.c:344:6: warning: If memory allocation fails, then there is a possible null pointer dereference: new_ME [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:341:36: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:341:36: note: Assignment 'new_ME=malloc(sizeof(struct MergedExon_t))', assigned value is 0
Rsubread/src/detection-calls.c:344:6: note: Null pointer dereference
Rsubread/src/detection-calls.c:361:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_ME [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:360:35: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:360:35: note: Assignment 'new_ME=malloc(sizeof(struct MergedExon_t))', assigned value is 0
Rsubread/src/detection-calls.c:361:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:362:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_ME [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:360:35: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:360:35: note: Assignment 'new_ME=malloc(sizeof(struct MergedExon_t))', assigned value is 0
Rsubread/src/detection-calls.c:362:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:363:5: warning: If memory allocation fails, then there is a possible null pointer dereference: new_ME [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:360:35: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:360:35: note: Assignment 'new_ME=malloc(sizeof(struct MergedExon_t))', assigned value is 0
Rsubread/src/detection-calls.c:363:5: note: Null pointer dereference
Rsubread/src/detection-calls.c:429:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:429:9: note: Null pointer dereference
Rsubread/src/detection-calls.c:431:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:431:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:432:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:432:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:433:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:433:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:435:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:435:9: note: Null pointer dereference
Rsubread/src/detection-calls.c:436:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:436:9: note: Null pointer dereference
Rsubread/src/detection-calls.c:437:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:437:9: note: Null pointer dereference
Rsubread/src/detection-calls.c:439:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:439:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:440:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:440:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:441:35: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:441:35: note: Null pointer dereference
Rsubread/src/detection-calls.c:443:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:443:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:444:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:444:36: note: Null pointer dereference
Rsubread/src/detection-calls.c:445:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:445:36: note: Null pointer dereference
Rsubread/src/detection-calls.c:446:27: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:446:27: note: Null pointer dereference
Rsubread/src/detection-calls.c:448:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:448:2: note: Null pointer dereference
Rsubread/src/detection-calls.c:449:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:449:36: note: Null pointer dereference
Rsubread/src/detection-calls.c:450:27: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/detection-calls.c:428:29: note: Assuming allocation function fails
Rsubread/src/detection-calls.c:428:29: note: Assignment 'ret=malloc(sizeof(struct DTCcontext_t))', assigned value is 0
Rsubread/src/detection-calls.c:450:27: note: Null pointer dereference
Rsubread/src/detection-calls.c:43:30: style: Parameter 'gene_name' can be declared as pointer to const. However it seems that 'DTCdo_add_feature' is a callback function, if 'gene_name' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/detection-calls.c:237:80: note: You might need to cast the function pointer here
Rsubread/src/detection-calls.c:43:30: note: Parameter 'gene_name' can be declared as pointer to const
Rsubread/src/detection-calls.c:62:69: style: Parameter 'me' can be declared as pointer to const. However it seems that 'DTCcompare_merge_genes' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/detection-calls.c:394:36: note: You might need to cast the function pointer here
Rsubread/src/detection-calls.c:62:69: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/detection-calls.c:63:17: style: Variable 'le' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:63:32: style: Variable 're' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:68:63: style: Parameter 'me' can be declared as pointer to const. However it seems that 'DTCcompare_exons' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/detection-calls.c:281:32: note: You might need to cast the function pointer here
Rsubread/src/detection-calls.c:68:63: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/detection-calls.c:69:14: style: Variable 'le' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:69:29: style: Variable 're' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:90:10: style: Variable 'fl' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:153:17: style: Variable 'gc_2int' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:159:47: style: Parameter 'hashed_obj' can be declared as pointer to const [constParameterPointer]
Rsubread/src/detection-calls.c:165:47: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/detection-calls.c:167:9: style: Variable 'bin2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:180:9: style: Variable 'tna' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:256:11: style: Variable 'memky' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:266:11: style: Variable 'tchro' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:293:11: style: Variable 'tmpky' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:310:12: style: Variable 'memky' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:329:16: style: Variable 'tmpexon' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:399:19: style: Variable 'geneints' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detection-calls.c:408:16: style: Variable 'top_start' is assigned a value that is never used. [unreadVariable]
Rsubread/src/detectionCall.c:393:20: style: Array index 'left' is used before limits check. [arrayIndexThenCheck]
Rsubread/src/detectionCall.c:226:4: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/detectionCall.c:227:5: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/detectionCall.c:228:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/detectionCall.c:231:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/detectionCall.c:148:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCall.c:183:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCall.c:259:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCall.c:302:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCall.c:432:11: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCall.c:102:9: warning: If memory allocation fails, then there is a possible null pointer dereference: SAM_file [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:94:27: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:94:13: note: Assignment 'SAM_file=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:102:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:104:9: warning: If memory allocation fails, then there is a possible null pointer dereference: simplified_SAM_file [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:95:38: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:95:24: note: Assignment 'simplified_SAM_file=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:104:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:105:9: warning: If memory allocation fails, then there is a possible null pointer dereference: simplified_SAM_file [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:95:38: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:95:24: note: Assignment 'simplified_SAM_file=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:105:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:107:9: warning: If memory allocation fails, then there is a possible null pointer dereference: sorted_simplified_SAM_file [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:96:45: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:96:31: note: Assignment 'sorted_simplified_SAM_file=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:107:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:108:9: warning: If memory allocation fails, then there is a possible null pointer dereference: sorted_simplified_SAM_file [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:96:45: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:96:31: note: Assignment 'sorted_simplified_SAM_file=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:108:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:110:9: warning: If memory allocation fails, then there is a possible null pointer dereference: annotation_exon_file [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:97:39: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:97:25: note: Assignment 'annotation_exon_file=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:110:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:112:9: warning: If memory allocation fails, then there is a possible null pointer dereference: annotation_ir_file [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:98:37: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:98:23: note: Assignment 'annotation_ir_file=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:112:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:114:9: warning: If memory allocation fails, then there is a possible null pointer dereference: mapping_result_exon [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:99:38: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:99:24: note: Assignment 'mapping_result_exon=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:114:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:115:9: warning: If memory allocation fails, then there is a possible null pointer dereference: mapping_result_exon [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:99:38: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:99:24: note: Assignment 'mapping_result_exon=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:115:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:117:9: warning: If memory allocation fails, then there is a possible null pointer dereference: mapping_result_ir [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:100:36: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:100:22: note: Assignment 'mapping_result_ir=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:117:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:118:9: warning: If memory allocation fails, then there is a possible null pointer dereference: mapping_result_ir [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:100:36: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:100:22: note: Assignment 'mapping_result_ir=(char*)malloc(300)', assigned value is 0
Rsubread/src/detectionCall.c:118:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:126:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:126:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:127:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:127:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:128:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:128:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:129:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:129:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:130:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:130:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:131:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:131:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:132:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:132:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:133:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:125:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:125:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCall.c:133:2: note: Null pointer dereference
Rsubread/src/detectionCall.c:223:27: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:221:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:221:9: note: Assignment 'line=(char*)malloc(len+1)', assigned value is 0
Rsubread/src/detectionCall.c:223:27: note: Null pointer dereference
Rsubread/src/detectionCall.c:223:38: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
Rsubread/src/detectionCall.c:218:13: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:218:13: note: Assignment 'fin=fopen(SAM_file,"r")', assigned value is 0
Rsubread/src/detectionCall.c:223:38: note: Null pointer dereference
Rsubread/src/detectionCall.c:224:6: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: line [nullPointerOutOfMemory]
Rsubread/src/detectionCall.c:221:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:221:9: note: Assignment 'line=(char*)malloc(len+1)', assigned value is 0
Rsubread/src/detectionCall.c:224:6: note: Null pointer dereference
Rsubread/src/detectionCall.c:351:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fout_exon [nullPointerOutOfResources]
Rsubread/src/detectionCall.c:349:25: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:349:25: note: Assignment 'fout_exon=fopen(mapping_result_exon,"w")', assigned value is 0
Rsubread/src/detectionCall.c:351:10: note: Null pointer dereference
Rsubread/src/detectionCall.c:356:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fout_exon [nullPointerOutOfResources]
Rsubread/src/detectionCall.c:349:25: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:349:25: note: Assignment 'fout_exon=fopen(mapping_result_exon,"w")', assigned value is 0
Rsubread/src/detectionCall.c:356:12: note: Null pointer dereference
Rsubread/src/detectionCall.c:359:9: warning: If resource allocation fails, then there is a possible null pointer dereference: fout_exon [nullPointerOutOfResources]
Rsubread/src/detectionCall.c:349:25: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:349:25: note: Assignment 'fout_exon=fopen(mapping_result_exon,"w")', assigned value is 0
Rsubread/src/detectionCall.c:359:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:365:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fout_ir [nullPointerOutOfResources]
Rsubread/src/detectionCall.c:364:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:364:23: note: Assignment 'fout_ir=fopen(mapping_result_ir,"w")', assigned value is 0
Rsubread/src/detectionCall.c:365:10: note: Null pointer dereference
Rsubread/src/detectionCall.c:370:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fout_ir [nullPointerOutOfResources]
Rsubread/src/detectionCall.c:364:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:364:23: note: Assignment 'fout_ir=fopen(mapping_result_ir,"w")', assigned value is 0
Rsubread/src/detectionCall.c:370:12: note: Null pointer dereference
Rsubread/src/detectionCall.c:373:9: warning: If resource allocation fails, then there is a possible null pointer dereference: fout_ir [nullPointerOutOfResources]
Rsubread/src/detectionCall.c:364:23: note: Assuming allocation function fails
Rsubread/src/detectionCall.c:364:23: note: Assignment 'fout_ir=fopen(mapping_result_ir,"w")', assigned value is 0
Rsubread/src/detectionCall.c:373:9: note: Null pointer dereference
Rsubread/src/detectionCall.c:144:7: style: Local variable 'current_chr_id' shadows outer variable [shadowVariable]
Rsubread/src/detectionCall.c:89:6: note: Shadowed declaration
Rsubread/src/detectionCall.c:144:7: note: Shadow variable
Rsubread/src/detectionCall.c:179:7: style: Local variable 'current_chr_id' shadows outer variable [shadowVariable]
Rsubread/src/detectionCall.c:89:6: note: Shadowed declaration
Rsubread/src/detectionCall.c:179:7: note: Shadow variable
Rsubread/src/detectionCall.c:92:26: style: Parameter 'dataset' can be declared as pointer to const [constParameterPointer]
Rsubread/src/detectionCall.c:92:41: style: Parameter 'exon_file' can be declared as pointer to const [constParameterPointer]
Rsubread/src/detectionCall.c:92:58: style: Parameter 'ir_file' can be declared as pointer to const [constParameterPointer]
Rsubread/src/detectionCall.c:92:73: style: Parameter 'temp_header' can be declared as pointer to const [constParameterPointer]
Rsubread/src/detectionCall.c:212:9: style: Variable 'read_chr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detectionCall.c:216:8: style: Variable 'readline' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detectionCall.c:149:22: error: Uninitialized variable: current_chr_id [legacyUninitvar]
Rsubread/src/detectionCall.c:184:22: error: Uninitialized variable: current_chr_id [legacyUninitvar]
Rsubread/src/detectionCallAnnotation.c:90:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCallAnnotation.c:124:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCallAnnotation.c:158:9: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/detectionCallAnnotation.c:68:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:68:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:69:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:69:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:70:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:70:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:71:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:71:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:72:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:72:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:73:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:73:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:74:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:74:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:75:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:67:23: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:67:8: note: Assignment 'new=(struct node*)malloc(sizeof(struct node))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:75:2: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:189:10: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:188:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:188:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:189:10: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:190:10: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:188:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:188:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:190:10: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:191:10: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:188:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:188:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:191:10: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:195:16: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:188:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:188:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:195:16: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:196:43: warning: If resource allocation fails, then there is a possible null pointer dereference: fseq [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:195:15: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:195:15: note: Assignment 'fseq=fopen(filename,"r")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:196:43: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:202:39: warning: If resource allocation fails, then there is a possible null pointer dereference: fseq [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:195:15: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:195:15: note: Assignment 'fseq=fopen(filename,"r")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:197:11: note: Assuming condition is false
Rsubread/src/detectionCallAnnotation.c:202:39: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:259:12: warning: If resource allocation fails, then there is a possible null pointer dereference: f_annotation_DCC_exon [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:252:37: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:252:37: note: Assignment 'f_annotation_DCC_exon=fopen(DCC_exon_GC_file,"w")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:259:12: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:262:9: warning: If resource allocation fails, then there is a possible null pointer dereference: f_annotation_DCC_exon [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:252:37: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:252:37: note: Assignment 'f_annotation_DCC_exon=fopen(DCC_exon_GC_file,"w")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:262:9: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:279:10: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:278:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:278:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:279:10: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:280:10: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:278:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:278:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:280:10: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:281:10: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:278:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:278:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:281:10: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:284:16: warning: If memory allocation fails, then there is a possible null pointer dereference: filename [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:278:28: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:278:14: note: Assignment 'filename=(char*)malloc(100*sizeof(char))', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:284:16: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:285:43: warning: If resource allocation fails, then there is a possible null pointer dereference: fseq [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:284:15: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:284:15: note: Assignment 'fseq=fopen(filename,"r")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:285:43: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:291:39: warning: If resource allocation fails, then there is a possible null pointer dereference: fseq [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:284:15: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:284:15: note: Assignment 'fseq=fopen(filename,"r")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:286:11: note: Assuming condition is false
Rsubread/src/detectionCallAnnotation.c:291:39: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:347:12: warning: If resource allocation fails, then there is a possible null pointer dereference: f_annotation_DCC_ir [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:340:35: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:340:35: note: Assignment 'f_annotation_DCC_ir=fopen(DCC_ir_GC_file,"w")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:347:12: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:350:9: warning: If resource allocation fails, then there is a possible null pointer dereference: f_annotation_DCC_ir [nullPointerOutOfResources]
Rsubread/src/detectionCallAnnotation.c:340:35: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:340:35: note: Assignment 'f_annotation_DCC_ir=fopen(DCC_ir_GC_file,"w")', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:350:9: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:379:9: warning: If memory allocation fails, then there is a possible null pointer dereference: DCC_exon_file [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:378:32: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:378:18: note: Assignment 'DCC_exon_file=(char*)malloc(100)', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:379:9: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:381:9: warning: If memory allocation fails, then there is a possible null pointer dereference: DCC_ir_file [nullPointerOutOfMemory]
Rsubread/src/detectionCallAnnotation.c:380:30: note: Assuming allocation function fails
Rsubread/src/detectionCallAnnotation.c:380:16: note: Assignment 'DCC_ir_file=(char*)malloc(100)', assigned value is 0
Rsubread/src/detectionCallAnnotation.c:381:9: note: Null pointer dereference
Rsubread/src/detectionCallAnnotation.c:86:7: style: Local variable 'DCC_current_chr_id' shadows outer variable [shadowVariable]
Rsubread/src/detectionCallAnnotation.c:55:6: note: Shadowed declaration
Rsubread/src/detectionCallAnnotation.c:86:7: note: Shadow variable
Rsubread/src/detectionCallAnnotation.c:120:7: style: Local variable 'DCC_current_chr_id' shadows outer variable [shadowVariable]
Rsubread/src/detectionCallAnnotation.c:55:6: note: Shadowed declaration
Rsubread/src/detectionCallAnnotation.c:120:7: note: Shadow variable
Rsubread/src/detectionCallAnnotation.c:196:10: style: Variable 'flin' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detectionCallAnnotation.c:251:8: style: Variable 'DCC_exon_GC_file' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detectionCallAnnotation.c:285:10: style: Variable 'flin' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detectionCallAnnotation.c:339:8: style: Variable 'DCC_ir_GC_file' can be declared as pointer to const [constVariablePointer]
Rsubread/src/detectionCallAnnotation.c:373:86: style: Parameter 'user_binsize' can be declared as pointer to const [constParameterPointer]
Rsubread/src/detectionCallAnnotation.c:91:22: error: Uninitialized variable: DCC_current_chr_id [legacyUninitvar]
Rsubread/src/detectionCallAnnotation.c:125:22: error: Uninitialized variable: DCC_current_chr_id [legacyUninitvar]
Rsubread/src/core.c:3412:3: error: Address of local auto-variable assigned to a function parameter. [autoVariables]
Rsubread/src/core.c:1880:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/core.c:3694:13: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
Rsubread/src/core.c:810:10: style: Condition 'wret==-1' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:800:13: note: Assignment 'wret=0', assigned value is 0
Rsubread/src/core.c:810:10: note: Condition 'wret==-1' is always false
Rsubread/src/core.c:1433:7: style: Condition '0&&FIXLENstrcmp("V0112_0155:7:1101:5279:29143#ATCACG",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:1566:8: style: Condition '0&&(memcmp(read_name,"V0112_0155:7:1104:17648:117432",28)==0||(this_event->event_small_side>2613701363-200&&this_event->event_small_side<2613701363+100))' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:1901:9: style: Condition '0&&is_funky' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:3207:10: style: Condition '0&&FIXLENstrcmp("R00000000181",read_name_1)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:3274:11: style: Condition '0&&FIXLENstrcmp("R00000003493",current_read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:3283:11: style: Condition '0&&FIXLENstrcmp("R00000003493",current_read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:3814:7: style: Condition '0&&!context->config.output_prefix[0]' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:4218:22: style: Condition 'init_paired_votes(context)' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:4218:22: note: Calling function 'init_paired_votes' returns 0
Rsubread/src/core.c:4218:22: note: Condition 'init_paired_votes(context)' is always false
Rsubread/src/core.c:4583:9: style: Condition '0&&FIXLENstrcmp("R000000007",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:4591:9: style: Condition '0&&FIXLENstrcmp("R000000007",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core.c:933:3: error: Memory leak: fline [memleak]
Rsubread/src/core.c:3078:3: error: Memory leak: read_text_1 [memleak]
Rsubread/src/core.c:3078:3: error: Memory leak: read_text_2 [memleak]
Rsubread/src/core.c:3078:3: error: Memory leak: qual_text_1 [memleak]
Rsubread/src/core.c:3078:3: error: Memory leak: qual_text_2 [memleak]
Rsubread/src/core.c:3078:3: error: Memory leak: vote_1 [memleak]
Rsubread/src/core.c:3078:3: error: Memory leak: vote_2 [memleak]
Rsubread/src/core.c:3078:3: error: Memory leak: vote_fg [memleak]
Rsubread/src/core.c:173:2: warning: If memory allocation fails, then there is a possible null pointer dereference: out_line_buff [nullPointerOutOfMemory]
Rsubread/src/core.c:172:23: note: Assuming allocation function fails
Rsubread/src/core.c:172:23: note: Assignment 'out_line_buff=malloc(1200)', assigned value is 0
Rsubread/src/core.c:173:2: note: Null pointer dereference
Rsubread/src/core.c:355:10: warning: If resource allocation fails, then there is a possible null pointer dereference: sumfp [nullPointerOutOfResources]
Rsubread/src/core.c:351:22: note: Assuming allocation function fails
Rsubread/src/core.c:351:22: note: Assignment 'sumfp=fopen(sumname,"w")', assigned value is 0
Rsubread/src/core.c:355:10: note: Null pointer dereference
Rsubread/src/core.c:357:10: warning: If resource allocation fails, then there is a possible null pointer dereference: sumfp [nullPointerOutOfResources]
Rsubread/src/core.c:351:22: note: Assuming allocation function fails
Rsubread/src/core.c:351:22: note: Assignment 'sumfp=fopen(sumname,"w")', assigned value is 0
Rsubread/src/core.c:357:10: note: Null pointer dereference
Rsubread/src/core.c:358:10: warning: If resource allocation fails, then there is a possible null pointer dereference: sumfp [nullPointerOutOfResources]
Rsubread/src/core.c:351:22: note: Assuming allocation function fails
Rsubread/src/core.c:351:22: note: Assignment 'sumfp=fopen(sumname,"w")', assigned value is 0
Rsubread/src/core.c:358:10: note: Null pointer dereference
Rsubread/src/core.c:359:10: warning: If resource allocation fails, then there is a possible null pointer dereference: sumfp [nullPointerOutOfResources]
Rsubread/src/core.c:351:22: note: Assuming allocation function fails
Rsubread/src/core.c:351:22: note: Assignment 'sumfp=fopen(sumname,"w")', assigned value is 0
Rsubread/src/core.c:359:10: note: Null pointer dereference
Rsubread/src/core.c:360:10: warning: If resource allocation fails, then there is a possible null pointer dereference: sumfp [nullPointerOutOfResources]
Rsubread/src/core.c:351:22: note: Assuming allocation function fails
Rsubread/src/core.c:351:22: note: Assignment 'sumfp=fopen(sumname,"w")', assigned value is 0
Rsubread/src/core.c:360:10: note: Null pointer dereference
Rsubread/src/core.c:884:9: warning: If memory allocation fails, then there is a possible null pointer dereference: global_context [nullPointerOutOfMemory]
Rsubread/src/core.c:883:44: note: Assuming allocation function fails
Rsubread/src/core.c:883:19: note: Assignment 'global_context=(struct global_context_t*)malloc(sizeof(struct global_context_t))', assigned value is 0
Rsubread/src/core.c:884:9: note: Null pointer dereference
Rsubread/src/core.c:892:5: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: global_context [nullPointerOutOfMemory]
Rsubread/src/core.c:883:44: note: Assuming allocation function fails
Rsubread/src/core.c:883:19: note: Assignment 'global_context=(struct global_context_t*)malloc(sizeof(struct global_context_t))', assigned value is 0
Rsubread/src/core.c:892:5: note: Null pointer dereference
Rsubread/src/core.c:892:54: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: global_context [nullPointerOutOfMemory]
Rsubread/src/core.c:883:44: note: Assuming allocation function fails
Rsubread/src/core.c:883:19: note: Assignment 'global_context=(struct global_context_t*)malloc(sizeof(struct global_context_t))', assigned value is 0
Rsubread/src/core.c:892:54: note: Null pointer dereference
Rsubread/src/core.c:3870:12: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: obuf [nullPointerOutOfMemory]
Rsubread/src/core.c:3855:23: note: Assuming allocation function fails
Rsubread/src/core.c:3855:23: note: Assignment 'obuf=malloc(10000+5000)', assigned value is 0
Rsubread/src/core.c:3870:12: note: Null pointer dereference
Rsubread/src/core.c:4852:9: warning: If memory allocation fails, then there is a possible null pointer dereference: fixed_len [nullPointerOutOfMemory]
Rsubread/src/core.c:4851:27: note: Assuming allocation function fails
Rsubread/src/core.c:4851:27: note: Assignment 'fixed_len=malloc(strlen(flen)+1)', assigned value is 0
Rsubread/src/core.c:4852:9: note: Null pointer dereference
Rsubread/src/flattenAnnotations.c:73:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/flattenAnnotations.c:335:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/flattenAnnotations.c:114:10: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_gene [nullPointerOutOfMemory]
Rsubread/src/flattenAnnotations.c:113:27: note: Assuming allocation function fails
Rsubread/src/flattenAnnotations.c:113:27: note: Assignment 'mem_gene=malloc(strlen(gene_name)+1)', assigned value is 0
Rsubread/src/flattenAnnotations.c:114:10: note: Null pointer dereference
Rsubread/src/flattenAnnotations.c:142:2: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_start_end [nullPointerOutOfMemory]
Rsubread/src/flattenAnnotations.c:141:30: note: Assuming allocation function fails
Rsubread/src/flattenAnnotations.c:141:30: note: Assignment 'mem_start_end=malloc(sizeof(int)*2)', assigned value is 0
Rsubread/src/flattenAnnotations.c:142:2: note: Null pointer dereference
Rsubread/src/flattenAnnotations.c:143:2: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_start_end [nullPointerOutOfMemory]
Rsubread/src/flattenAnnotations.c:141:30: note: Assuming allocation function fails
Rsubread/src/flattenAnnotations.c:141:30: note: Assignment 'mem_start_end=malloc(sizeof(int)*2)', assigned value is 0
Rsubread/src/flattenAnnotations.c:143:2: note: Null pointer dereference
Rsubread/src/flattenAnnotations.c:177:9: warning: If memory allocation fails, then there is a possible null pointer dereference: continue_after_an_edge [nullPointerOutOfMemory]
Rsubread/src/flattenAnnotations.c:176:40: note: Assuming allocation function fails
Rsubread/src/flattenAnnotations.c:176:40: note: Assignment 'continue_after_an_edge=malloc(edge_before_me_List->numOfElements-1)', assigned value is 0
Rsubread/src/flattenAnnotations.c:177:9: note: Null pointer dereference
Rsubread/src/flattenAnnotations.c:215:3: warning: If memory allocation fails, then there is a possible null pointer dereference: curr_2i [nullPointerOutOfMemory]
Rsubread/src/flattenAnnotations.c:212:20: note: Assuming allocation function fails
Rsubread/src/flattenAnnotations.c:212:20: note: Assignment 'curr_2i=malloc(sizeof(int)*2)', assigned value is 0
Rsubread/src/flattenAnnotations.c:215:3: note: Null pointer dereference
Rsubread/src/flattenAnnotations.c:216:3: warning: If memory allocation fails, then there is a possible null pointer dereference: curr_2i [nullPointerOutOfMemory]
Rsubread/src/flattenAnnotations.c:212:20: note: Assuming allocation function fails
Rsubread/src/flattenAnnotations.c:212:20: note: Assignment 'curr_2i=malloc(sizeof(int)*2)', assigned value is 0
Rsubread/src/flattenAnnotations.c:216:3: note: Null pointer dereference
Rsubread/src/flattenAnnotations.c:268:8: warning: If memory allocation fails, then there is a possible null pointer dereference: strand_ptr [nullPointerOutOfMemory]
Rsubread/src/flattenAnnotations.c:264:39: note: Assuming allocation function fails
Rsubread/src/flattenAnnotations.c:264:39: note: Assignment 'local_ge_chro_strand=strdup(ge_chro_strand)', assigned value is 0
Rsubread/src/flattenAnnotations.c:265:23: note: Assignment 'strand_ptr=local_ge_chro_strand', assigned value is 0
Rsubread/src/flattenAnnotations.c:268:8: note: Null pointer dereference
Rsubread/src/core.c:3417:102: style: Same expression 'global_context->config.do_breakpoint_detection' found multiple times in chain of '||' operators. [duplicateExpression]
Rsubread/src/core.c:3725:93: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary]
Rsubread/src/core.c:4245:86: style: Same expression 'context->config.do_breakpoint_detection' found multiple times in chain of '||' operators. [duplicateExpression]
Rsubread/src/core.c:4255:86: style: Same expression 'context->config.do_breakpoint_detection' found multiple times in chain of '||' operators. [duplicateExpression]
Rsubread/src/flattenAnnotations.c:124:10: style: Variable 'old_ch_st' can be declared as pointer to const [constVariablePointer]
Rsubread/src/flattenAnnotations.c:148:79: style: Parameter 'me' can be declared as pointer to const. However it seems that 'flatAnno_do_anno_merge_one_array_compare' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/flattenAnnotations.c:228:27: note: You might need to cast the function pointer here
Rsubread/src/flattenAnnotations.c:148:79: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/flattenAnnotations.c:149:8: style: Variable 'iL' can be declared as pointer to const [constVariablePointer]
Rsubread/src/flattenAnnotations.c:149:18: style: Variable 'iR' can be declared as pointer to const [constVariablePointer]
Rsubread/src/flattenAnnotations.c:160:9: style: Variable 'curr_2i' can be declared as pointer to const [constVariablePointer]
Rsubread/src/flattenAnnotations.c:183:10: style: Variable 'curr_2i' can be declared as pointer to const [constVariablePointer]
Rsubread/src/flattenAnnotations.c:232:9: style: Variable 'curr_2i' can be declared as pointer to const [constVariablePointer]
Rsubread/src/flattenAnnotations.c:249:26: style: Parameter 'L' can be declared as pointer to const. However it seems that 'flatme_strcmp' is a callback function, if 'L' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/flattenAnnotations.c:258:34: note: You might need to cast the function pointer here
Rsubread/src/flattenAnnotations.c:249:26: note: Parameter 'L' can be declared as pointer to const
Rsubread/src/flattenAnnotations.c:249:36: style: Parameter 'R' can be declared as pointer to const. However it seems that 'flatme_strcmp' is a callback function, if 'R' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/flattenAnnotations.c:258:34: note: You might need to cast the function pointer here
Rsubread/src/flattenAnnotations.c:249:36: note: Parameter 'R' can be declared as pointer to const
Rsubread/src/flattenAnnotations.c:249:51: style: Parameter 'me' can be declared as pointer to const. However it seems that 'flatme_strcmp' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/flattenAnnotations.c:258:34: note: You might need to cast the function pointer here
Rsubread/src/flattenAnnotations.c:249:51: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/flattenAnnotations.c:263:10: style: Variable 'ge_chro_strand' can be declared as pointer to const [constVariablePointer]
Rsubread/src/flattenAnnotations.c:274:10: style: Variable 'start_end_2i' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:239:19: style: Variable 'content_len' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/core.c:238:19: note: content_len is assigned
Rsubread/src/core.c:239:19: note: content_len is overwritten
Rsubread/src/core.c:3541:42: style:inconclusive: Function 'read_chunk_circles' argument 1 names different: declaration 'context' definition 'global_context'. [funcArgNamesDifferent]
Rsubread/src/core.h:630:43: note: Function 'read_chunk_circles' argument 1 names different: declaration 'context' definition 'global_context'.
Rsubread/src/core.c:3541:42: note: Function 'read_chunk_circles' argument 1 names different: declaration 'context' definition 'global_context'.
Rsubread/src/core.c:4482:46: style:inconclusive: Function 'term_strncpy' argument 3 names different: declaration 'max_dst_memory' definition 'max_dst_mem'. [funcArgNamesDifferent]
Rsubread/src/core.h:663:46: note: Function 'term_strncpy' argument 3 names different: declaration 'max_dst_memory' definition 'max_dst_mem'.
Rsubread/src/core.c:4482:46: note: Function 'term_strncpy' argument 3 names different: declaration 'max_dst_memory' definition 'max_dst_mem'.
Rsubread/src/core.c:4507:257: style:inconclusive: Function 'chimeric_cigar_parts' argument 10 names different: declaration 'out_read_lens' definition 'perfect_lens'. [funcArgNamesDifferent]
Rsubread/src/core.h:678:258: note: Function 'chimeric_cigar_parts' argument 10 names different: declaration 'out_read_lens' definition 'perfect_lens'.
Rsubread/src/core.c:4507:257: note: Function 'chimeric_cigar_parts' argument 10 names different: declaration 'out_read_lens' definition 'perfect_lens'.
Rsubread/src/core.c:4733:33: style:inconclusive: Function 'basic_sort' argument 2 names different: declaration 'arr_size' definition 'items'. [funcArgNamesDifferent]
Rsubread/src/core.h:682:32: note: Function 'basic_sort' argument 2 names different: declaration 'arr_size' definition 'items'.
Rsubread/src/core.c:4733:33: note: Function 'basic_sort' argument 2 names different: declaration 'arr_size' definition 'items'.
Rsubread/src/core.c:4815:240: style:inconclusive: Function 'test_PE_and_same_chro_align' argument 9 names different: declaration 'rname' definition 'read_name'. [funcArgNamesDifferent]
Rsubread/src/core.c:2380:240: note: Function 'test_PE_and_same_chro_align' argument 9 names different: declaration 'rname' definition 'read_name'.
Rsubread/src/core.c:4815:240: note: Function 'test_PE_and_same_chro_align' argument 9 names different: declaration 'rname' definition 'read_name'.
Rsubread/src/core.c:4821:154: style:inconclusive: Function 'test_PE_and_same_chro' argument 6 names different: declaration 'rlen1' definition 'read_len_1'. [funcArgNamesDifferent]
Rsubread/src/core.h:690:155: note: Function 'test_PE_and_same_chro' argument 6 names different: declaration 'rlen1' definition 'read_len_1'.
Rsubread/src/core.c:4821:154: note: Function 'test_PE_and_same_chro' argument 6 names different: declaration 'rlen1' definition 'read_len_1'.
Rsubread/src/core.c:4821:170: style:inconclusive: Function 'test_PE_and_same_chro' argument 7 names different: declaration 'rlen2' definition 'read_len_2'. [funcArgNamesDifferent]
Rsubread/src/core.h:690:166: note: Function 'test_PE_and_same_chro' argument 7 names different: declaration 'rlen2' definition 'read_len_2'.
Rsubread/src/core.c:4821:170: note: Function 'test_PE_and_same_chro' argument 7 names different: declaration 'rlen2' definition 'read_len_2'.
Rsubread/src/core.c:4849:25: style:inconclusive: Function 'FIXLENstrcmp' argument 1 names different: declaration 'fixed_len' definition 'flen'. [funcArgNamesDifferent]
Rsubread/src/core.h:692:25: note: Function 'FIXLENstrcmp' argument 1 names different: declaration 'fixed_len' definition 'flen'.
Rsubread/src/core.c:4849:25: note: Function 'FIXLENstrcmp' argument 1 names different: declaration 'fixed_len' definition 'flen'.
Rsubread/src/core.c:184:20: style: Local variable 'content_len' shadows outer variable [shadowVariable]
Rsubread/src/core.c:171:6: note: Shadowed declaration
Rsubread/src/core.c:184:20: note: Shadow variable
Rsubread/src/core.c:2704:8: style: Local variable 'is_second_read' shadows outer variable [shadowVariable]
Rsubread/src/core.c:2551:7: note: Shadowed declaration
Rsubread/src/core.c:2704:8: note: Shadow variable
Rsubread/src/core.c:495:74: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:929:9: style: Variable 'env_no_sort' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:947:10: style: Variable 'is_ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:1003:11: style: Variable 'is_ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:1067:12: style: Variable 'bufr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:1232:36: style: Parameter 'CIGAR' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1286:45: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1308:48: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1325:39: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1325:74: style: Parameter 'current_result' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1325:97: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1325:132: style: Parameter 'read_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1350:61: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1601:41: style: Parameter 'remainder_cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1622:22: style: Parameter 'cig' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1644:26: style: Variable 'this_rec' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:1645:26: style: Variable 'mate_rec' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:1718:34: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1791:44: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1837:82: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1888:150: style: Parameter 'raw_r1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:1888:210: style: Parameter 'raw_r2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2214:121: style: Parameter 'result' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2252:41: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2252:76: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2260:47: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2260:82: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2441:44: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2443:9: style: Variable 'r1_cigar' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:2451:9: style: Variable 'r2_cigar' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:3022:84: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:3022:107: style: Parameter 'qual' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:3040:21: style: Variable 'this_r' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:3042:22: style: Variable 'better_r' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:3327:47: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:3691:14: style: Variable 'timeinfo' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:3904:61: style: Parameter 'anno_chro' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:3911:11: style: Variable 'tab_anno_chro' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:3960:14: style: Variable 'alias_index_to_annot' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:3964:9: style: Variable 'annot_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:4033:10: style: Variable 'reads_per_chunk' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:4034:10: style: Variable 'remove_beighbour' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core.c:4373:30: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:4404:28: style: Parameter 'bincigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:4757:50: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:4849:25: style: Parameter 'flen' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:4849:38: style: Parameter 'rname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core.c:2831:19: style: int result is assigned to long long variable. If the variable is long long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
Rsubread/src/core.c:1081:16: warning: Uninitialized variable: temp_file_name [uninitvar]
Rsubread/src/core.c:1058:5: note: Assuming condition is false
Rsubread/src/core.c:1081:16: note: Uninitialized variable: temp_file_name
Rsubread/src/core.c:1373:29: style: Variable 'linear_cursor' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core.c:1388:19: style: Variable 'linear_cursor' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core.c:1443:25: style: Variable 'chimeric_sections' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core.c:2289:20: style: Variable 'best_read_id' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core.c:2536:27: style: Variable 'r1_align_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory]
Rsubread/src/core.c:2537:27: style: Variable 'r2_align_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory]
Rsubread/src/core.c:2539:29: style: Variable 'r1_subjunc_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory]
Rsubread/src/core.c:2540:29: style: Variable 'r2_subjunc_result_buffer' is allocated memory that is never used. [unusedAllocatedMemory]
Rsubread/src/core.c:259:10: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
Rsubread/src/fullscan.c:38:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/fullscan.c:169:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
Rsubread/src/fullscan.c:68:28: style: Parameter 'c1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/fullscan.c:68:39: style: Parameter 'c2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gen_rand_reads.c:165:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
Rsubread/src/gen_rand_reads.c:881:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/gene-algorithms.c:1391:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCK_REALTIME [valueFlowBailoutIncompleteVar]
Rsubread/src/gene-algorithms.c:2487:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/gen_rand_reads.c:976:21: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
Rsubread/src/gen_rand_reads.c:808:5: error: Common realloc mistake: 'lbuf' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/gen_rand_reads.c:560:11: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_name [nullPointerOutOfMemory]
Rsubread/src/gen_rand_reads.c:559:19: note: Assuming allocation function fails
Rsubread/src/gen_rand_reads.c:559:19: note: Assignment 'seq_name=malloc(rlength)', assigned value is 0
Rsubread/src/gen_rand_reads.c:560:11: note: Null pointer dereference
Rsubread/src/gen_rand_reads.c:681:24: warning: Either the condition 'NULL==seqexp_str' is redundant or there is possible null pointer dereference: seqexp_str. [nullPointerRedundantCheck]
Rsubread/src/gen_rand_reads.c:677:11: note: Assuming that condition 'NULL==seqexp_str' is not redundant
Rsubread/src/gen_rand_reads.c:681:24: note: Null pointer dereference
Rsubread/src/gen_rand_reads.c:689:10: warning: If memory allocation fails, then there is a possible null pointer dereference: seqname_buf [nullPointerOutOfMemory]
Rsubread/src/gen_rand_reads.c:688:30: note: Assuming allocation function fails
Rsubread/src/gen_rand_reads.c:688:30: note: Assignment 'seqname_buf=malloc(strlen(seqname)+1)', assigned value is 0
Rsubread/src/gen_rand_reads.c:689:10: note: Null pointer dereference
Rsubread/src/gen_rand_reads.c:729:11: warning: If memory allocation fails, then there is a possible null pointer dereference: qstr [nullPointerOutOfMemory]
Rsubread/src/gen_rand_reads.c:728:24: note: Assuming allocation function fails
Rsubread/src/gen_rand_reads.c:728:24: note: Assignment 'qstr=malloc(rline)', assigned value is 0
Rsubread/src/gen_rand_reads.c:729:11: note: Null pointer dereference
Rsubread/src/gen_rand_reads.c:730:7: warning: If memory allocation fails, then there is a possible null pointer dereference: qstr [nullPointerOutOfMemory]
Rsubread/src/gen_rand_reads.c:728:24: note: Assuming allocation function fails
Rsubread/src/gen_rand_reads.c:728:24: note: Assignment 'qstr=malloc(rline)', assigned value is 0
Rsubread/src/gen_rand_reads.c:730:7: note: Null pointer dereference
Rsubread/src/gen_rand_reads.c:795:11: warning: If memory allocation fails, then there is a possible null pointer dereference: seq_name [nullPointerOutOfMemory]
Rsubread/src/gen_rand_reads.c:789:21: note: Assuming allocation function fails
Rsubread/src/gen_rand_reads.c:789:21: note: Assignment 'seq_name=malloc(strlen(clinebuf))', assigned value is 0
Rsubread/src/gen_rand_reads.c:790:19: note: Assuming condition is false
Rsubread/src/gen_rand_reads.c:795:11: note: Null pointer dereference
Rsubread/src/gen_rand_reads.c:997:7: style: Local variable 'ret' shadows outer variable [shadowVariable]
Rsubread/src/gen_rand_reads.c:985:6: note: Shadowed declaration
Rsubread/src/gen_rand_reads.c:997:7: note: Shadow variable
Rsubread/src/gen_rand_reads.c:159:61: style: Parameter 'qua' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gen_rand_reads.c:173:56: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gen_rand_reads.c:173:130: style: Parameter 'seq_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gen_rand_reads.c:348:10: style: Variable 'seq_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:411:9: style: Variable 'seq_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:553:11: style: Variable 'had_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:599:10: style: Variable 'seqnam' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:600:10: style: Variable 'md5str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:675:10: style: Variable 'seqname' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:676:10: style: Variable 'seqexp_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:691:10: style: Variable 'had_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:770:12: style: Variable 'had_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:830:10: style: Variable 'had_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gen_rand_reads.c:1000:7: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:1374:54: error: Array 'current_vote->pos[30][24]' accessed at index current_vote->pos[-1][-1], which is out of bounds. [negativeIndex]
Rsubread/src/core-junction.c:1451:43: note: Assignment 'best_R1_j=-1', assigned value is -1
Rsubread/src/core-junction.c:1453:21: note: Assuming condition is false
Rsubread/src/core-junction.c:1472:70: note: Calling function 'simple_copy_vote_to_result', 4th argument 'best_R1_j' value is -1
Rsubread/src/core-junction.c:1374:54: note: Negative array index
Rsubread/src/core-junction.c:1376:132: error: Array 'current_vote->indel_recorder[30][24][21]' accessed at index current_vote->indel_recorder[-1][-1], which is out of bounds. [negativeIndex]
Rsubread/src/core-junction.c:1451:43: note: Assignment 'best_R1_j=-1', assigned value is -1
Rsubread/src/core-junction.c:1453:21: note: Assuming condition is false
Rsubread/src/core-junction.c:1472:70: note: Calling function 'simple_copy_vote_to_result', 4th argument 'best_R1_j' value is -1
Rsubread/src/core-junction.c:1376:132: note: Negative array index
Rsubread/src/core-junction.c:1379:52: error: Array 'current_vote->masks[30][24]' accessed at index current_vote->masks[-1][-1], which is out of bounds. [negativeIndex]
Rsubread/src/core-junction.c:1451:43: note: Assignment 'best_R1_j=-1', assigned value is -1
Rsubread/src/core-junction.c:1453:21: note: Assuming condition is false
Rsubread/src/core-junction.c:1472:70: note: Calling function 'simple_copy_vote_to_result', 4th argument 'best_R1_j' value is -1
Rsubread/src/core-junction.c:1379:52: note: Negative array index
Rsubread/src/core-junction.c:5217:30: style: Array index 'kk' is used before limits check. [arrayIndexThenCheck]
Rsubread/src/core-junction.c:1948:26: style: Expression is always false because 'else if' condition matches previous condition at line 1946. [multiCondition]
Rsubread/src/core-junction.c:2888:30: warning: Identical condition 'last_matched_base_index<0', second condition is always false [identicalConditionAfterEarlyExit]
Rsubread/src/core-junction.c:2885:29: note: If condition 'last_matched_base_index<0' is true, the function will return/exit
Rsubread/src/core-junction.c:2888:30: note: Testing identical condition 'last_matched_base_index<0'
Rsubread/src/core-junction.c:3384:23: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
Rsubread/src/core-junction.c:3373:22: note: outer condition: mismatch_bases<=applied_mismatch
Rsubread/src/core-junction.c:3384:23: note: opposite inner condition: mismatch_bases>applied_mismatch
Rsubread/src/core-junction.c:179:9: style: Condition '0&&FIXLENstrcmp("R010442852",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:204:9: style: Condition '0&&FIXLENstrcmp("R010442852",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:217:11: style: Condition '0&&FIXLENstrcmp("R00000001230",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:312:7: style: Condition '0&&FIXLENstrcmp("simulated.11420793",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:336:8: style: Condition '0&&FIXLENstrcmp("R010442852",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:405:7: style: Condition '0&&FIXLENstrcmp("R010442852",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:479:15: style: Condition '0&&explain_context->best_matching_bases==explain_context->tmp_total_matched_bases' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:484:8: style: Condition '0&&FIXLENstrcmp("R010442852",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:541:7: style: Condition '0&&FIXLENstrcmp("R010442852",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:568:24: style: Condition 'is_same_best&&0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:679:11: style: Condition '0&&FIXLENstrcmp("R00000001230",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1107:11: style: Condition '0&&FIXLENstrcmp("R002403247",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1124:10: style: Condition '0&&FIXLENstrcmp("R002403247",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1176:13: style: Condition '0&&1018082==pair_number' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1197:12: style: Condition '0&&FIXLENstrcmp("R000404427",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1267:12: style: Condition '0&&(FIXLENstrcmp("R006232475",read_name)==0)' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1275:10: style: Condition '0&&(FIXLENstrcmp("R006232475",read_name)==0)' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1293:11: style: Condition '0&&1018082==pair_number' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1311:8: style: Condition '0&&memcmp("V0112_0155:7:1101:1173:2204",read_name,26)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1421:7: style: Condition '1||max_cluster_size_r1==3' is always true [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1428:9: style: Condition '0&&FIXLENstrcmp("R00000003493",read_name_1)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1600:8: style: Condition '0&&FIXLENstrcmp("V0112_0155:7:1101:13762:2349#ACTTGA",rname)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1644:8: style: Condition '0&&(!scan_to_tail)' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1679:8: style: Condition '0&&scan_to_tail' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1715:6: style: Condition '0&&best_best_occurance>0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1886:19: style: Condition 'highest_score>0' is always true [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1856:45: note: Assuming that condition 'highest_score>160-159' is not redundant
Rsubread/src/core-junction.c:1886:19: note: Condition 'highest_score>0' is always true
Rsubread/src/core-junction.c:1917:8: style: Condition '0&&front_score>0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1987:9: style: Condition '0&&front_mismatched_bases<1' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:1999:9: style: Condition '0&&tail_mismatched_bases<1' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2099:8: style: Condition '0&&FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA",rname)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2121:7: style: Condition '0&&FIXLENstrcmp("V0112_0155:7:1101:12618:2466",rname)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2140:8: style: Condition '0&&FIXLENstrcmp("chr14:105",out1pos)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2239:8: style: Condition '0&&FIXLENstrcmp("R00000003493",read_name_1)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2249:8: style: Condition '0&&FIXLENstrcmp("R00000003493",read_name_1)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2639:7: style: Condition '0&&FIXLENstrcmp("simulated.24700032",explain_context.read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2743:7: style: Condition '0&&FIXLENstrcmp("R000002689",explain_context.read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2753:14: style: Condition '0&&FIXLENstrcmp("R00000001230",explain_context.read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2760:7: style: Condition '0&&FIXLENstrcmp("R_chr901_932716_91M1D9M",explain_context.read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2772:7: style: Condition '0&&FIXLENstrcmp("SRR3439488.572382",explain_context.read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2891:30: style: Condition 'last_matched_base_index>=0' is always true [knownConditionTrueFalse]
Rsubread/src/core-junction.c:2885:29: note: Assuming that condition 'last_matched_base_index<0' is not redundant
Rsubread/src/core-junction.c:2891:30: note: Condition 'last_matched_base_index>=0' is always true
Rsubread/src/core-junction.c:2998:11: style: Condition '0&&FIXLENstrcmp("NS500643:556:HGTMTBGXB:4:13403:18179:8012",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3142:8: style: Condition '0&&FIXLENstrcmp("NS500643:556:HGTMTBGXB:4:13403:18179:8012",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3202:9: style: Condition '0&&FIXLENstrcmp("simulated.11420793",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3330:10: style: Condition '0&&explain_context->result_back_junction_numbers[back_i]+explain_context->result_front_junction_numbers[front_i]<=2' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3333:9: style: Condition '0&&FIXLENstrcmp("simulated.11420793",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3350:9: style: Condition '0&&FIXLENstrcmp("R00000001230",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3365:9: style: Condition '0&&FIXLENstrcmp("R00000001122",explain_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3696:7: style: Condition '0&&FIXLENstrcmp("R006856515",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3734:8: style: Condition '0&&FIXLENstrcmp("R006856515",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3825:8: style: Condition '0&&FIXLENstrcmp("R006856515",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:3965:8: style: Condition '0&&FIXLENstrcmp("R003738400",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:4110:10: style: Condition '0&&FIXLENstrcmp("R000000052",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:4807:39: style: Condition 'chro_name!=best_chro_name' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:4797:18: note: Assuming that condition 'chro_name!=best_chro_name' is not redundant
Rsubread/src/core-junction.c:4807:39: note: Condition 'chro_name!=best_chro_name' is always false
Rsubread/src/core-junction.c:5239:11: style: Condition '0&&strcmp("MISEQ:13:000000000-A1H1M:1:1112:12194:5511",rname)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:5291:15: style: Condition '0&&strcmp("MISEQ:13:000000000-A1H1M:1:1112:12194:5511",rname)==0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:5701:21: style: Return value 'nSupD1mates>0' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:5659:20: note: Assignment 'nSupD1mates=0', assigned value is 0
Rsubread/src/core-junction.c:5701:21: note: Return value 'nSupD1mates>0' is always false
Rsubread/src/core-junction.c:6018:9: style: Condition '0&&frag_A_no==143736' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:6351:7: style: Condition 'is_passed_YZ' is always false [knownConditionTrueFalse]
Rsubread/src/core-junction.c:5659:20: note: Assignment 'nSupD1mates=0', assigned value is 0
Rsubread/src/core-junction.c:6350:46: note: Calling function 'breakpoint_YZ_supported' returns 0
Rsubread/src/core-junction.c:6350:46: note: Assignment 'is_passed_YZ=breakpoint_YZ_supported(global_context,brkYno,brkZno,s1_selected_list,s1_list_items,s2_selected_list,s2_list_items)', assigned value is 0
Rsubread/src/core-junction.c:6351:7: note: Condition 'is_passed_YZ' is always false
Rsubread/src/core-junction.c:4191:10: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-junction.c:4191:10: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/core-junction.c:4191:10: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/core-junction.c:4201:11: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-junction.c:4201:11: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/core-junction.c:4201:11: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/core-junction.c:4275:4: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
Rsubread/src/core-junction.c:957:30: warning: If memory allocation fails, then there is a possible null pointer dereference: merge_target [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:941:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:941:44: note: Assignment 'merge_target=malloc(sizeof(struct vote_combination_t)*(items+items2))', assigned value is 0
Rsubread/src/core-junction.c:957:30: note: Null pointer dereference
Rsubread/src/core-junction.c:2858:45: warning: If memory allocation fails, then there is a possible null pointer dereference: read_text [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:2989:43: note: Assuming allocation function fails
Rsubread/src/core-junction.c:2989:43: note: Assignment 'reversed_first_section_text=malloc(1210)', assigned value is 0
Rsubread/src/core-junction.c:2993:99: note: Calling function 'find_soft_clipping', 4th argument 'reversed_first_section_text' value is 0
Rsubread/src/core-junction.c:2858:45: note: Null pointer dereference
Rsubread/src/core-junction.c:2960:14: warning: If memory allocation fails, then there is a possible null pointer dereference: reversed_first_section_text [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:2959:43: note: Assuming allocation function fails
Rsubread/src/core-junction.c:2959:43: note: Assignment 'reversed_first_section_text=malloc(1210)', assigned value is 0
Rsubread/src/core-junction.c:2960:14: note: Null pointer dereference
Rsubread/src/core-junction.c:2991:14: warning: If memory allocation fails, then there is a possible null pointer dereference: reversed_first_section_text [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:2989:43: note: Assuming allocation function fails
Rsubread/src/core-junction.c:2989:43: note: Assignment 'reversed_first_section_text=malloc(1210)', assigned value is 0
Rsubread/src/core-junction.c:2991:14: note: Null pointer dereference
Rsubread/src/core-junction.c:5456:9: warning: If memory allocation fails, then there is a possible null pointer dereference: is_C_used [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5455:27: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5455:27: note: Assignment 'is_C_used=malloc(sizeof(char)*listC->fragments)', assigned value is 0
Rsubread/src/core-junction.c:5456:9: note: Null pointer dereference
Rsubread/src/core-junction.c:5484:7: warning: If memory allocation fails, then there is a possible null pointer dereference: is_C_used [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5455:27: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5455:27: note: Assignment 'is_C_used=malloc(sizeof(char)*listC->fragments)', assigned value is 0
Rsubread/src/core-junction.c:5484:7: note: Null pointer dereference
Rsubread/src/core-junction.c:5853:10: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5853:10: note: Null pointer dereference
Rsubread/src/core-junction.c:5854:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5854:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5855:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5855:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5856:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5856:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5857:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5857:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5858:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5858:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5859:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5859:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5860:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5852:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5852:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5860:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5920:10: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5920:10: note: Null pointer dereference
Rsubread/src/core-junction.c:5921:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5921:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5922:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5922:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5923:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5923:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5924:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5924:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5925:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5925:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5926:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5926:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5927:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5927:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5928:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5928:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5929:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5929:3: note: Null pointer dereference
Rsubread/src/core-junction.c:5930:3: warning: If memory allocation fails, then there is a possible null pointer dereference: new_res [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:5919:44: note: Assuming allocation function fails
Rsubread/src/core-junction.c:5919:44: note: Assignment 'new_res=malloc(sizeof(struct translocation_result_t))', assigned value is 0
Rsubread/src/core-junction.c:5930:3: note: Null pointer dereference
Rsubread/src/core-junction.c:6397:12: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6397:12: note: Null pointer dereference
Rsubread/src/core-junction.c:6399:5: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6399:5: note: Null pointer dereference
Rsubread/src/core-junction.c:6400:5: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6400:5: note: Null pointer dereference
Rsubread/src/core-junction.c:6402:6: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6402:6: note: Null pointer dereference
Rsubread/src/core-junction.c:6403:6: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6403:6: note: Null pointer dereference
Rsubread/src/core-junction.c:6404:6: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6404:6: note: Null pointer dereference
Rsubread/src/core-junction.c:6406:6: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6406:6: note: Null pointer dereference
Rsubread/src/core-junction.c:6407:6: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6407:6: note: Null pointer dereference
Rsubread/src/core-junction.c:6408:6: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6408:6: note: Null pointer dereference
Rsubread/src/core-junction.c:6410:5: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6410:5: note: Null pointer dereference
Rsubread/src/core-junction.c:6411:5: warning: If memory allocation fails, then there is a possible null pointer dereference: inv_res_new [nullPointerOutOfMemory]
Rsubread/src/core-junction.c:6396:46: note: Assuming allocation function fails
Rsubread/src/core-junction.c:6396:46: note: Assignment 'inv_res_new=malloc(sizeof(struct chromosome_event_t))', assigned value is 0
Rsubread/src/core-junction.c:6411:5: note: Null pointer dereference
Rsubread/src/core-junction.c:3277:8: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
Rsubread/src/core-junction.c:3284:8: note: Found duplicate branches for 'if' and 'else'.
Rsubread/src/core-junction.c:3277:8: note: Found duplicate branches for 'if' and 'else'.
Rsubread/src/core-junction.c:4167:84: style: Same expression on both sides of '-'. [duplicateExpression]
Rsubread/src/core-junction.c:4308:90: style: Same expression on both sides of '-'. [duplicateExpression]
Rsubread/src/core-junction.c:5504:39: style: Same expression on both sides of '-'. [duplicateExpression]
Rsubread/src/core-junction.c:1251:26: style: Variable 'right_indel_offset' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/core-junction.c:1240:27: note: right_indel_offset is assigned
Rsubread/src/core-junction.c:1251:26: note: right_indel_offset is overwritten
Rsubread/src/core-junction.c:1251:26: style: Variable 'right_indel_offset' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/core-junction.c:1244:27: note: right_indel_offset is assigned
Rsubread/src/core-junction.c:1251:26: note: right_indel_offset is overwritten
Rsubread/src/core-junction.c:4467:12: style: Variable 'max_score' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/core-junction.c:4420:13: note: max_score is assigned
Rsubread/src/core-junction.c:4467:12: note: max_score is overwritten
Rsubread/src/core-junction.c:4862:26: style: Variable '*read_coverage_start' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/core-junction.c:4859:26: note: *read_coverage_start is assigned
Rsubread/src/core-junction.c:4862:26: note: *read_coverage_start is overwritten
Rsubread/src/core-junction.c:4863:24: style: Variable '*read_coverage_end' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/core-junction.c:4860:24: note: *read_coverage_end is assigned
Rsubread/src/core-junction.c:4863:24: note: *read_coverage_end is overwritten
Rsubread/src/core-junction.c:6302:8: style: Unsigned expression 'event_body_Y->event_large_side-q_res_2->selected_position' can't be negative so it is unnecessary to test it. [unsignedPositive]
Rsubread/src/core-junction.c:588:253: style:inconclusive: Function 'search_events_to_back' argument 9 names different: declaration 'suggested_movements' definition 'suggested_movement'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:140:253: note: Function 'search_events_to_back' argument 9 names different: declaration 'suggested_movements' definition 'suggested_movement'.
Rsubread/src/core-junction.c:588:253: note: Function 'search_events_to_back' argument 9 names different: declaration 'suggested_movements' definition 'suggested_movement'.
Rsubread/src/core-junction.c:1787:333: style:inconclusive: Function 'align_cluster' argument 14 names different: declaration 'ii_path' definition 'best_ii_path'. [funcArgNamesDifferent]
Rsubread/src/core-junction.c:1371:333: note: Function 'align_cluster' argument 14 names different: declaration 'ii_path' definition 'best_ii_path'.
Rsubread/src/core-junction.c:1787:333: note: Function 'align_cluster' argument 14 names different: declaration 'ii_path' definition 'best_ii_path'.
Rsubread/src/core-junction.c:1787:353: style:inconclusive: Function 'align_cluster' argument 15 names different: declaration 'jj_path' definition 'best_jj_path'. [funcArgNamesDifferent]
Rsubread/src/core-junction.c:1371:348: note: Function 'align_cluster' argument 15 names different: declaration 'jj_path' definition 'best_jj_path'.
Rsubread/src/core-junction.c:1787:353: note: Function 'align_cluster' argument 15 names different: declaration 'jj_path' definition 'best_jj_path'.
Rsubread/src/core-junction.c:1787:373: style:inconclusive: Function 'align_cluster' argument 16 names different: declaration 'masks' definition 'best_masks'. [funcArgNamesDifferent]
Rsubread/src/core-junction.c:1371:363: note: Function 'align_cluster' argument 16 names different: declaration 'masks' definition 'best_masks'.
Rsubread/src/core-junction.c:1787:373: note: Function 'align_cluster' argument 16 names different: declaration 'masks' definition 'best_masks'.
Rsubread/src/core-junction.c:1787:391: style:inconclusive: Function 'align_cluster' argument 17 names different: declaration 'path_len' definition 'best_path_length'. [funcArgNamesDifferent]
Rsubread/src/core-junction.c:1371:376: note: Function 'align_cluster' argument 17 names different: declaration 'path_len' definition 'best_path_length'.
Rsubread/src/core-junction.c:1787:391: note: Function 'align_cluster' argument 17 names different: declaration 'path_len' definition 'best_path_length'.
Rsubread/src/core-junction.c:2616:120: style:inconclusive: Function 'explain_read' argument 3 names different: declaration 'realigns' definition 'final_realignments'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:130:120: note: Function 'explain_read' argument 3 names different: declaration 'realigns' definition 'final_realignments'.
Rsubread/src/core-junction.c:2616:120: note: Function 'explain_read' argument 3 names different: declaration 'realigns' definition 'final_realignments'.
Rsubread/src/core-junction.c:2616:231: style:inconclusive: Function 'explain_read' argument 8 names different: declaration 'qual' definition 'qual_text'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:130:220: note: Function 'explain_read' argument 8 names different: declaration 'qual' definition 'qual_text'.
Rsubread/src/core-junction.c:2616:231: note: Function 'explain_read' argument 8 names different: declaration 'qual' definition 'qual_text'.
Rsubread/src/core-junction.c:3158:167: style:inconclusive: Function 'finalise_explain_CIGAR' argument 4 names different: declaration 'realigns' definition 'final_realignments'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:138:167: note: Function 'finalise_explain_CIGAR' argument 4 names different: declaration 'realigns' definition 'final_realignments'.
Rsubread/src/core-junction.c:3158:167: note: Function 'finalise_explain_CIGAR' argument 4 names different: declaration 'realigns' definition 'final_realignments'.
Rsubread/src/core-junction.c:3519:119: style:inconclusive: Function 'is_ambiguous_voting' argument 4 names different: declaration 'max_vote' definition 'selected_vote'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:153:119: note: Function 'is_ambiguous_voting' argument 4 names different: declaration 'max_vote' definition 'selected_vote'.
Rsubread/src/core-junction.c:3519:119: note: Function 'is_ambiguous_voting' argument 4 names different: declaration 'max_vote' definition 'selected_vote'.
Rsubread/src/core-junction.c:3573:107: style:inconclusive: Function 'donor_jumped_score' argument 3 names different: declaration 'left_virtualHead_abs_offset' definition 'small_virtualHead_abs_offset'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:107: note: Function 'donor_jumped_score' argument 3 names different: declaration 'left_virtualHead_abs_offset' definition 'small_virtualHead_abs_offset'.
Rsubread/src/core-junction.c:3573:107: note: Function 'donor_jumped_score' argument 3 names different: declaration 'left_virtualHead_abs_offset' definition 'small_virtualHead_abs_offset'.
Rsubread/src/core-junction.c:3573:150: style:inconclusive: Function 'donor_jumped_score' argument 4 names different: declaration 'right_virtualHead_abs_offset' definition 'large_virtualHead_abs_offset'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:149: note: Function 'donor_jumped_score' argument 4 names different: declaration 'right_virtualHead_abs_offset' definition 'large_virtualHead_abs_offset'.
Rsubread/src/core-junction.c:3573:150: note: Function 'donor_jumped_score' argument 4 names different: declaration 'right_virtualHead_abs_offset' definition 'large_virtualHead_abs_offset'.
Rsubread/src/core-junction.c:3573:249: style:inconclusive: Function 'donor_jumped_score' argument 9 names different: declaration 'is_left_half_negative' definition 'is_small_half_negative'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:248: note: Function 'donor_jumped_score' argument 9 names different: declaration 'is_left_half_negative' definition 'is_small_half_negative'.
Rsubread/src/core-junction.c:3573:249: note: Function 'donor_jumped_score' argument 9 names different: declaration 'is_left_half_negative' definition 'is_small_half_negative'.
Rsubread/src/core-junction.c:3573:277: style:inconclusive: Function 'donor_jumped_score' argument 10 names different: declaration 'is_right_half_negative' definition 'is_large_half_negative'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:275: note: Function 'donor_jumped_score' argument 10 names different: declaration 'is_right_half_negative' definition 'is_large_half_negative'.
Rsubread/src/core-junction.c:3573:277: note: Function 'donor_jumped_score' argument 10 names different: declaration 'is_right_half_negative' definition 'is_large_half_negative'.
Rsubread/src/core-junction.c:3573:305: style:inconclusive: Function 'donor_jumped_score' argument 11 names different: declaration 'is_left_part_on_left_as_reversed' definition 'small_half_on_left_reversed'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:303: note: Function 'donor_jumped_score' argument 11 names different: declaration 'is_left_part_on_left_as_reversed' definition 'small_half_on_left_reversed'.
Rsubread/src/core-junction.c:3573:305: note: Function 'donor_jumped_score' argument 11 names different: declaration 'is_left_part_on_left_as_reversed' definition 'small_half_on_left_reversed'.
Rsubread/src/core-junction.c:3573:388: style:inconclusive: Function 'donor_jumped_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:391: note: Function 'donor_jumped_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'.
Rsubread/src/core-junction.c:3573:388: note: Function 'donor_jumped_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'.
Rsubread/src/core-junction.c:3573:424: style:inconclusive: Function 'donor_jumped_score' argument 15 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:413: note: Function 'donor_jumped_score' argument 15 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'.
Rsubread/src/core-junction.c:3573:424: note: Function 'donor_jumped_score' argument 15 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'.
Rsubread/src/core-junction.c:3573:464: style:inconclusive: Function 'donor_jumped_score' argument 16 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:148:440: note: Function 'donor_jumped_score' argument 16 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'.
Rsubread/src/core-junction.c:3573:464: note: Function 'donor_jumped_score' argument 16 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'.
Rsubread/src/core-junction.c:3672:176: style:inconclusive: Function 'donor_score' argument 5 names different: declaration 'left_indels' definition 'left_indel_offset'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:146:176: note: Function 'donor_score' argument 5 names different: declaration 'left_indels' definition 'left_indel_offset'.
Rsubread/src/core-junction.c:3672:176: note: Function 'donor_score' argument 5 names different: declaration 'left_indels' definition 'left_indel_offset'.
Rsubread/src/core-junction.c:3672:199: style:inconclusive: Function 'donor_score' argument 6 names different: declaration 'right_indels' definition 'right_indel_offset'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:146:193: note: Function 'donor_score' argument 6 names different: declaration 'right_indels' definition 'right_indel_offset'.
Rsubread/src/core-junction.c:3672:199: note: Function 'donor_score' argument 6 names different: declaration 'right_indels' definition 'right_indel_offset'.
Rsubread/src/core-junction.c:3672:361: style:inconclusive: Function 'donor_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:146:349: note: Function 'donor_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'.
Rsubread/src/core-junction.c:3672:361: note: Function 'donor_score' argument 14 names different: declaration 'is_donor_found' definition 'is_donor_found_or_annotation'.
Rsubread/src/core-junction.c:3672:397: style:inconclusive: Function 'donor_score' argument 15 names different: declaration 'inserted_bases' definition 'final_inserted_bases'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:146:371: note: Function 'donor_score' argument 15 names different: declaration 'inserted_bases' definition 'final_inserted_bases'.
Rsubread/src/core-junction.c:3672:397: note: Function 'donor_score' argument 15 names different: declaration 'inserted_bases' definition 'final_inserted_bases'.
Rsubread/src/core-junction.c:3672:425: style:inconclusive: Function 'donor_score' argument 16 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:146:393: note: Function 'donor_score' argument 16 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'.
Rsubread/src/core-junction.c:3672:425: note: Function 'donor_score' argument 16 names different: declaration 'small_side_inc_coor' definition 'small_side_increasing_coordinate'.
Rsubread/src/core-junction.c:3672:465: style:inconclusive: Function 'donor_score' argument 17 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'. [funcArgNamesDifferent]
Rsubread/src/core-junction.h:146:420: note: Function 'donor_score' argument 17 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'.
Rsubread/src/core-junction.c:3672:465: note: Function 'donor_score' argument 17 names different: declaration 'large_side_inc_coor' definition 'large_side_increasing_coordinate'.
Rsubread/src/core-junction.c:4226:43: style:inconclusive: Function 'write_inversion_results_final' argument 1 names different: declaration 'key' definition 'bukey'. [funcArgNamesDifferent]
Rsubread/src/core-junction.c:4137:43: note: Function 'write_inversion_results_final' argument 1 names different: declaration 'key' definition 'bukey'.
Rsubread/src/core-junction.c:4226:43: note: Function 'write_inversion_results_final' argument 1 names different: declaration 'key' definition 'bukey'.
Rsubread/src/core-junction.c:4251:47: style:inconclusive: Function 'write_translocation_results_final' argument 1 names different: declaration 'key' definition 'bukey'. [funcArgNamesDifferent]
Rsubread/src/core-junction.c:4136:47: note: Function 'write_translocation_results_final' argument 1 names different: declaration 'key' definition 'bukey'.
Rsubread/src/core-junction.c:4251:47: note: Function 'write_translocation_results_final' argument 1 names different: declaration 'key' definition 'bukey'.
Rsubread/src/core-junction.c:1657:10: style: Local variable 'nch' shadows outer variable [shadowVariable]
Rsubread/src/core-junction.c:1607:22: note: Shadowed declaration
Rsubread/src/core-junction.c:1657:10: note: Shadow variable
Rsubread/src/core-junction.c:1666:10: style: Local variable 'nch' shadows outer variable [shadowVariable]
Rsubread/src/core-junction.c:1607:22: note: Shadowed declaration
Rsubread/src/core-junction.c:1666:10: note: Shadow variable
Rsubread/src/core-junction.c:1692:10: style: Local variable 'nch' shadows outer variable [shadowVariable]
Rsubread/src/core-junction.c:1607:22: note: Shadowed declaration
Rsubread/src/core-junction.c:1692:10: note: Shadow variable
Rsubread/src/core-junction.c:1701:10: style: Local variable 'nch' shadows outer variable [shadowVariable]
Rsubread/src/core-junction.c:1607:22: note: Shadowed declaration
Rsubread/src/core-junction.c:1701:10: note: Shadow variable
Rsubread/src/core-junction.c:2217:62: style: Local variable 'i' shadows outer variable [shadowVariable]
Rsubread/src/core-junction.c:2209:21: note: Shadowed declaration
Rsubread/src/core-junction.c:2217:62: note: Shadow variable
Rsubread/src/core-junction.c:2217:66: style: Local variable 'j' shadows outer variable [shadowVariable]
Rsubread/src/core-junction.c:2209:23: note: Shadowed declaration
Rsubread/src/core-junction.c:2217:66: note: Shadow variable
Rsubread/src/core-junction.c:2324:9: style: Local variable 'is_PE_distance' shadows outer function [shadowFunction]
Rsubread/src/core-junction.c:814:5: note: Shadowed declaration
Rsubread/src/core-junction.c:2324:9: note: Shadow variable
Rsubread/src/core-junction.c:5298:33: style: Local variable 'event_space' shadows outer variable [shadowVariable]
Rsubread/src/core-junction.c:5157:23: note: Shadowed declaration
Rsubread/src/core-junction.c:5298:33: note: Shadow variable
Rsubread/src/core-junction.c:81:78: style: Parameter 'event' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:88:87: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:784:54: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:784:89: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:789:50: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:814:39: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:837:47: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:889:44: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:889:79: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:889:109: style: Parameter 'votes' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:908:42: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:962:40: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:962:75: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:962:110: style: Parameter 'junc_res' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:1050:49: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:1050:84: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:1224:29: style: Variable 'indel_recorder' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:1338:85: style: Parameter 'r1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:1338:108: style: Parameter 'r2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:1362:41: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:1362:82: style: Parameter 'cl' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:1442:28: style: Variable 'shifted_result_R1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:1443:28: style: Variable 'shifted_result_R2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:1488:28: style: Variable 'shifted_result_R' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:1545:8: style: Variable 'ii_array' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:1546:8: style: Variable 'jj_array' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:2019:38: style: Parameter 'small_bases' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2019:58: style: Parameter 'large_bases' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2243:23: style: Variable 'old_result' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:2299:24: style: Variable 'old_result' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:2506:9: style: Variable 'current_r_cursor' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:2507:22: style: Variable 'current_alignment_tmp' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:2508:22: style: Variable 'current_junction_tmp' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:2535:43: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:66: style: Parameter 'rname1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:81: style: Parameter 'chr1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:143: style: Parameter 'cigar1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:158: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:171: style: Parameter 'rname2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:186: style: Parameter 'chr2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:248: style: Parameter 'cigar2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:2535:263: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:3454:35: style: Parameter 'ch1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:3454:47: style: Parameter 'ch2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:3469:35: style: Parameter 'ch1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:3469:47: style: Parameter 'ch2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:3534:19: style: Variable 'big_margin_record' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:4141:20: style: Variable 'indel_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:4288:20: style: Variable 'indel_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:4363:30: style: Parameter 'ch1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:4363:42: style: Parameter 'ch2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:4383:107: style: Parameter 'read_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:4383:125: style: Parameter 'qualityb0' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:4738:578: style: Parameter 'max_indel_recorder' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:5429:22: style: Variable 'f_res' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5430:22: style: Variable 'mate_res' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5452:87: style: Parameter 'res_A1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:5452:114: style: Parameter 'res_A2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:5464:39: style: Variable 'res_Cc' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5464:72: style: Variable 'res_Bb' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5562:59: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:5661:24: style: Variable 'fragno_Dmates' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5677:23: style: Variable 'res_to_support_small_edge' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5678:23: style: Variable 'res_to_support_large_edge' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5726:24: style: Variable 'event_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5810:20: style: Variable 'indel_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:5811:23: style: Variable 'event_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6006:23: style: Variable 'q_res' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6193:24: style: Variable 'q_res' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6257:25: style: Variable 'res_D1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6258:25: style: Variable 'res_D2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6260:25: style: Variable 'res_E1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6261:25: style: Variable 'res_E2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6306:28: style: Variable 'event_body_Z' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6431:20: style: Variable 'indel_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:6438:24: style: Variable 'event_body' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:1827:29: warning: Uninitialized variable: is_second_vote_array [uninitvar]
Rsubread/src/core-junction.c:1796:18: note: Assuming condition is false
Rsubread/src/core-junction.c:1827:29: note: Uninitialized variable: is_second_vote_array
Rsubread/src/core-junction.c:6003:48: error: Memory is allocated but not initialized: s1_ptrs [uninitdata]
Rsubread/src/core-junction.c:6003:40: error: Memory is allocated but not initialized: s2_ptrs [uninitdata]
Rsubread/src/core-junction.c:6190:41: error: Memory is allocated but not initialized: s2_ptrs [uninitdata]
Rsubread/src/core-junction.c:6191:49: error: Memory is allocated but not initialized: s2_poses [uninitdata]
Rsubread/src/core-junction.c:6195:64: error: Memory is allocated but not initialized: s2_result_ptr_list [uninitdata]
Rsubread/src/core-junction.c:48:15: style: struct member 'select_junction_record_t::piece_main_abs_offset' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:49:15: style: struct member 'select_junction_record_t::piece_minor_abs_offset' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:50:6: style: struct member 'select_junction_record_t::piece_main_masks' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:51:8: style: struct member 'select_junction_record_t::piece_main_coverage_start' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:52:8: style: struct member 'select_junction_record_t::piece_main_coverage_end' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:54:8: style: struct member 'select_junction_record_t::piece_main_hamming_match' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:55:8: style: struct member 'select_junction_record_t::piece_main_read_quality' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:56:8: style: struct member 'select_junction_record_t::piece_minor_hamming_match' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:57:8: style: struct member 'select_junction_record_t::piece_minor_read_quality' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:58:6: style: struct member 'select_junction_record_t::piece_minor_score' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:59:8: style: struct member 'select_junction_record_t::intron_length' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:61:22: style: struct member 'select_junction_record_t::piece_main_indel_record' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:62:17: style: struct member 'select_junction_record_t::piece_main_indels' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:63:17: style: struct member 'select_junction_record_t::piece_minor_indel_offset' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:64:21: style: struct member 'select_junction_record_t::piece_main_votes' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:65:21: style: struct member 'select_junction_record_t::piece_minor_votes' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:67:8: style: struct member 'select_junction_record_t::piece_minor_coverage_start' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:68:8: style: struct member 'select_junction_record_t::piece_minor_coverage_end' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:69:8: style: struct member 'select_junction_record_t::split_point' is never used. [unusedStructMember]
Rsubread/src/gene-value-index.c:382:6: style: The if condition is the same as the previous if condition [duplicateCondition]
Rsubread/src/gene-value-index.c:375:6: note: First condition
Rsubread/src/gene-value-index.c:382:6: note: Second condition
Rsubread/src/core-junction.c:70:7: style: struct member 'select_junction_record_t::inserted_bases' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:71:7: style: struct member 'select_junction_record_t::is_GT_AG_donors' is never used. [unusedStructMember]
Rsubread/src/gene-value-index.c:29:85: style:inconclusive: Function 'gvindex_init' argument 3 names different: declaration 'all_bases_estm' definition 'total_bases_estimated'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:27:85: note: Function 'gvindex_init' argument 3 names different: declaration 'all_bases_estm' definition 'total_bases_estimated'.
Rsubread/src/gene-value-index.c:29:85: note: Function 'gvindex_init' argument 3 names different: declaration 'all_bases_estm' definition 'total_bases_estimated'.
Rsubread/src/gene-value-index.c:109:82: style:inconclusive: Function 'gvindex_match' argument 3 names different: declaration 'base_value' definition 'base_values'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:40:82: note: Function 'gvindex_match' argument 3 names different: declaration 'base_value' definition 'base_values'.
Rsubread/src/gene-value-index.c:109:82: note: Function 'gvindex_match' argument 3 names different: declaration 'base_value' definition 'base_values'.
Rsubread/src/gene-value-index.c:135:81: style:inconclusive: Function 'gvindex_set' argument 3 names different: declaration 'base_value' definition 'base_values'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:29:82: note: Function 'gvindex_set' argument 3 names different: declaration 'base_value' definition 'base_values'.
Rsubread/src/gene-value-index.c:135:81: note: Function 'gvindex_set' argument 3 names different: declaration 'base_value' definition 'base_values'.
Rsubread/src/gene-value-index.c:277:163: style:inconclusive: Function 'match_indel_chro_to_front' argument 8 names different: declaration 'max_test_len' definition 'max_test_length'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:56:162: note: Function 'match_indel_chro_to_front' argument 8 names different: declaration 'max_test_len' definition 'max_test_length'.
Rsubread/src/gene-value-index.c:277:163: note: Function 'match_indel_chro_to_front' argument 8 names different: declaration 'max_test_len' definition 'max_test_length'.
Rsubread/src/gene-value-index.c:416:112: style:inconclusive: Function 'match_indel_table_to_front' argument 4 names different: declaration 'pos' definition 'first_base_pos'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:59:112: note: Function 'match_indel_table_to_front' argument 4 names different: declaration 'pos' definition 'first_base_pos'.
Rsubread/src/gene-value-index.c:416:112: note: Function 'match_indel_table_to_front' argument 4 names different: declaration 'pos' definition 'first_base_pos'.
Rsubread/src/gene-value-index.c:530:110: style:inconclusive: Function 'match_indel_table_to_back' argument 4 names different: declaration 'pos' definition 'last_base_pos'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:60:111: note: Function 'match_indel_table_to_back' argument 4 names different: declaration 'pos' definition 'last_base_pos'.
Rsubread/src/gene-value-index.c:530:110: note: Function 'match_indel_table_to_back' argument 4 names different: declaration 'pos' definition 'last_base_pos'.
Rsubread/src/gene-value-index.c:749:146: style:inconclusive: Function 'match_chro_support' argument 7 names different: declaration 'qual_str' definition 'qual_txt'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:47:146: note: Function 'match_chro_support' argument 7 names different: declaration 'qual_str' definition 'qual_txt'.
Rsubread/src/gene-value-index.c:749:146: note: Function 'match_chro_support' argument 7 names different: declaration 'qual_str' definition 'qual_txt'.
Rsubread/src/gene-value-index.c:1037:142: style:inconclusive: Function 'match_chro_maxerror' argument 7 names different: declaration 'maxerror' definition 'max_error'. [funcArgNamesDifferent]
Rsubread/src/gene-value-index.h:50:142: note: Function 'match_chro_maxerror' argument 7 names different: declaration 'maxerror' definition 'max_error'.
Rsubread/src/gene-value-index.c:1037:142: note: Function 'match_chro_maxerror' argument 7 names different: declaration 'maxerror' definition 'max_error'.
Rsubread/src/gene-value-index.c:46:75: style: Parameter 'index' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-value-index.c:231:32: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-value-index.c:352:32: style: Parameter 'indel_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-value-index.c:399:20: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
Rsubread/src/core-junction.c:72:7: style: struct member 'select_junction_record_t::is_donor_found_or_annotation' is never used. [unusedStructMember]
Rsubread/src/gene-value-index.c:466:21: style: Variable 'this_record' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gene-value-index.c:587:21: style: Variable 'this_record' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gene-value-index.c:749:33: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-value-index.c:749:146: style: Parameter 'qual_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-value-index.c:856:23: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-value-index.c:1037:32: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
Rsubread/src/core-junction.c:74:7: style: struct member 'select_junction_record_t::is_break_even' is never used. [unusedStructMember]
Rsubread/src/core-junction.c:738:32: style: Variable 'this_round_junction_scanned' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:2822:47: style: Variable 'removed_base_index' is assigned a value that is never used. [unreadVariable]
Rsubread/src/hashtable.c:190:67: debug: Function::addArguments found argument 'L_elem' with varid 0. [varid0]
Rsubread/src/hashtable.c:1029:67: debug: Function::addArguments found argument 'key' with varid 0. [varid0]
Rsubread/src/core-junction.c:3164:28: style: Variable 'to_be_supported_count' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:3166:37: style: Variable 'total_perfect_matched_sections' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:3255:36: style: Variable 'total_perfect_matched_sections' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:3748:23: style: Variable 'inserted_bases' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:4996:21: style: Variable 'best_select_votes' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5154:20: style: Variable 'window_cursor' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5439:24: style: Variable 'f_negative' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5440:21: style: Variable 'mate_negative' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5728:24: style: Variable 'small_dist' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5728:69: style: Variable 'large_dist' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5729:14: style: Variable 'small_dist' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5730:14: style: Variable 'large_dist' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:5798:14: style: Variable 'found_PQR' is assigned a value that is never used. [unreadVariable]
Rsubread/src/core-junction.c:6274:27: style: Variable 'cand_YZ_breakpoints' is assigned a value that is never used. [unreadVariable]
Rsubread/src/hashtable.c:28:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
Rsubread/src/hashtable.c:193:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compare_L_minus_R [valueFlowBailoutIncompleteVar]
Rsubread/src/hashtable.c:83:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:82:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:82:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:83:9: note: Null pointer dereference
Rsubread/src/hashtable.c:84:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:82:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:82:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:84:2: note: Null pointer dereference
Rsubread/src/hashtable.c:85:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:82:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:82:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:85:2: note: Null pointer dereference
Rsubread/src/hashtable.c:91:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:91:9: note: Null pointer dereference
Rsubread/src/hashtable.c:92:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:92:2: note: Null pointer dereference
Rsubread/src/hashtable.c:93:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:93:2: note: Null pointer dereference
Rsubread/src/hashtable.c:94:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:94:2: note: Null pointer dereference
Rsubread/src/hashtable.c:94:45: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:94:45: note: Null pointer dereference
Rsubread/src/hashtable.c:95:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:95:9: note: Null pointer dereference
Rsubread/src/hashtable.c:95:64: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:95:64: note: Null pointer dereference
Rsubread/src/hashtable.c:96:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
Rsubread/src/hashtable.c:96:2: note: Null pointer dereference
Rsubread/src/hashtable.c:186:38: warning: If memory allocation fails, then there is a possible null pointer dereference: merged [nullPointerOutOfMemory]
Rsubread/src/hashtable.c:169:25: note: Assuming allocation function fails
Rsubread/src/hashtable.c:169:25: note: Assignment 'merged=malloc(sizeof(void*)*(items+items2))', assigned value is 0
Rsubread/src/hashtable.c:186:38: note: Null pointer dereference
Rsubread/src/hashtable.c:969:37: style:inconclusive: Function 'isProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'. [funcArgNamesDifferent]
Rsubread/src/hashtable.c:23:37: note: Function 'isProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'.
Rsubread/src/hashtable.c:969:37: note: Function 'isProbablePrime' argument 1 names different: declaration 'number' definition 'oddNumber'.
Rsubread/src/hashtable.c:47:38: style: Parameter 'list' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:47:51: style: Parameter 'who' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:139:37: style: Parameter 'L_elem' can be declared as pointer to const. However it seems that 'ArrayListSort_comp_pntr' is a callback function, if 'L_elem' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/hashtable.c:193:52: note: You might need to cast the function pointer here
Rsubread/src/hashtable.c:139:37: note: Parameter 'L_elem' can be declared as pointer to const
Rsubread/src/hashtable.c:139:52: style: Parameter 'R_elem' can be declared as pointer to const. However it seems that 'ArrayListSort_comp_pntr' is a callback function, if 'R_elem' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/hashtable.c:193:52: note: You might need to cast the function pointer here
Rsubread/src/hashtable.c:139:52: note: Parameter 'R_elem' can be declared as pointer to const
Rsubread/src/hashtable.c:139:72: style: Parameter 'me' can be declared as pointer to const. However it seems that 'ArrayListSort_comp_pntr' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/hashtable.c:193:52: note: You might need to cast the function pointer here
Rsubread/src/hashtable.c:139:72: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/hashtable.c:201:38: style: Parameter 'L_elem' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:201:53: style: Parameter 'R_elem' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:201:73: style: Parameter 'me' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:205:35: style: Parameter 'L_elem' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:205:50: style: Parameter 'R_elem' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:205:70: style: Parameter 'me' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:269:47: style: Parameter 'va' can be declared as pointer to const. However it seems that 'StringTableReverse_Run' is a callback function, if 'va' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/hashtable.c:279:26: note: You might need to cast the function pointer here
Rsubread/src/hashtable.c:269:47: note: Parameter 'va' can be declared as pointer to const
Rsubread/src/hashtable.c:298:45: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:981:55: style: Parameter 'hashTable' can be declared as pointer to const [constParameterPointer]
Rsubread/src/hashtable.c:1047:44: style: Parameter 'Lv' can be declared as pointer to const. However it seems that 'HashTableSortedIndexes_cmp_idx' is a callback function, if 'Lv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/hashtable.c:1069:21: note: You might need to cast the function pointer here
Rsubread/src/hashtable.c:1047:44: note: Parameter 'Lv' can be declared as pointer to const
Rsubread/src/hashtable.c:1047:55: style: Parameter 'Rv' can be declared as pointer to const. However it seems that 'HashTableSortedIndexes_cmp_idx' is a callback function, if 'Rv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/hashtable.c:1069:21: note: You might need to cast the function pointer here
Rsubread/src/hashtable.c:1047:55: note: Parameter 'Rv' can be declared as pointer to const
Rsubread/src/hashtable.c:1049:14: style: Variable 'k2int_tab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/hashtable.c:1050:9: style: Variable 'Lhash' can be declared as pointer to const [constVariablePointer]
Rsubread/src/hashtable.c:1051:9: style: Variable 'Rhash' can be declared as pointer to const [constVariablePointer]
Rsubread/src/hashtable.c:1052:9: style: Variable 'large_first' can be declared as pointer to const [constVariablePointer]
Rsubread/src/hashtable.c:43:84: portability: 'ArrayListGet(arr,x1)' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/hashtable.c:300:29: portability: 'oldv' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/index-builder.c:1053:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/input-blc.c:57:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DT_REG [valueFlowBailoutIncompleteVar]
Rsubread/src/input-blc.c:483:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
Rsubread/src/index-builder.c:106:3: error: Memory leak: read_offsets [memleak]
Rsubread/src/index-builder.c:106:3: error: Memory leak: read_names [memleak]
Rsubread/src/index-builder.c:106:3: error: Memory leak: ginp [memleak]
Rsubread/src/index-builder.c:112:3: error: Memory leak: read_offsets [memleak]
Rsubread/src/index-builder.c:112:3: error: Memory leak: read_names [memleak]
Rsubread/src/index-builder.c:112:3: error: Memory leak: ginp [memleak]
Rsubread/src/index-builder.c:118:3: error: Memory leak: read_offsets [memleak]
Rsubread/src/index-builder.c:118:3: error: Memory leak: read_names [memleak]
Rsubread/src/index-builder.c:118:3: error: Memory leak: ginp [memleak]
Rsubread/src/index-builder.c:125:115: error: Memory leak: read_offsets [memleak]
Rsubread/src/index-builder.c:125:115: error: Memory leak: read_names [memleak]
Rsubread/src/index-builder.c:125:115: error: Memory leak: ginp [memleak]
Rsubread/src/index-builder.c:126:71: error: Memory leak: read_offsets [memleak]
Rsubread/src/index-builder.c:126:71: error: Memory leak: read_names [memleak]
Rsubread/src/index-builder.c:126:71: error: Memory leak: ginp [memleak]
Rsubread/src/index-builder.c:819:3: error: Memory leak: line_buf [memleak]
Rsubread/src/index-builder.c:819:3: error: Memory leak: read_head_buf [memleak]
Rsubread/src/index-builder.c:249:6: error: Common realloc mistake: 'read_offsets' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/index-builder.c:250:6: error: Common realloc mistake: 'read_names' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/index-builder.c:144:9: warning: If memory allocation fails, then there is a possible null pointer dereference: fn [nullPointerOutOfMemory]
Rsubread/src/index-builder.c:141:20: note: Assuming allocation function fails
Rsubread/src/index-builder.c:141:20: note: Assignment 'fn=malloc(3100)', assigned value is 0
Rsubread/src/index-builder.c:144:9: note: Null pointer dereference
Rsubread/src/index-builder.c:536:9: warning: If memory allocation fails, then there is a possible null pointer dereference: fn [nullPointerOutOfMemory]
Rsubread/src/index-builder.c:534:20: note: Assuming allocation function fails
Rsubread/src/index-builder.c:534:20: note: Assignment 'fn=malloc(3100)', assigned value is 0
Rsubread/src/index-builder.c:536:9: note: Null pointer dereference
Rsubread/src/index-builder.c:914:12: warning: If memory allocation fails, then there is a possible null pointer dereference: keymem [nullPointerOutOfMemory]
Rsubread/src/index-builder.c:913:27: note: Assuming allocation function fails
Rsubread/src/index-builder.c:913:27: note: Assignment 'keymem=malloc(chro_name_end)', assigned value is 0
Rsubread/src/index-builder.c:914:12: note: Null pointer dereference
Rsubread/src/index-builder.c:358:64: style: Same value in both branches of ternary operator. [duplicateValueTernary]
Rsubread/src/index-builder.c:371:95: style: Same value in both branches of ternary operator. [duplicateValueTernary]
Rsubread/src/index-builder.c:543:7: style: Local variable 'i' shadows outer variable [shadowVariable]
Rsubread/src/index-builder.c:488:19: note: Shadowed declaration
Rsubread/src/index-builder.c:543:7: note: Shadow variable
Rsubread/src/index-builder.c:960:10: style: Local variable 'line_buf_len' shadows outer variable [shadowVariable]
Rsubread/src/index-builder.c:859:8: note: Shadowed declaration
Rsubread/src/index-builder.c:960:10: note: Shadow variable
Rsubread/src/index-builder.c:56:47: style: Parameter 'bucket_sizes' can be declared as pointer to const [constParameterPointer]
Rsubread/src/index-builder.c:76:35: style: Parameter 'key' can be declared as pointer to const. However it seems that 'save_none_informative' is a callback function, if 'key' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/index-builder.c:452:34: note: You might need to cast the function pointer here
Rsubread/src/index-builder.c:76:35: note: Parameter 'key' can be declared as pointer to const
Rsubread/src/index-builder.c:76:47: style: Parameter 'hashed_obj' can be declared as pointer to const. However it seems that 'save_none_informative' is a callback function, if 'hashed_obj' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/index-builder.c:452:34: note: You might need to cast the function pointer here
Rsubread/src/index-builder.c:76:47: note: Parameter 'hashed_obj' can be declared as pointer to const
Rsubread/src/index-builder.c:715:54: style: Parameter 'fcc' can be declared as pointer to const [constParameterPointer]
Rsubread/src/index-builder.c:715:66: style: Parameter 'msg' can be declared as pointer to const [constParameterPointer]
Rsubread/src/index-builder.c:719:39: style: Parameter 'FN' can be declared as pointer to const [constParameterPointer]
Rsubread/src/index-builder.c:719:112: style: Parameter 'msg' can be declared as pointer to const [constParameterPointer]
Rsubread/src/index-builder.c:762:10: style: Variable 'ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/index-builder.c:786:10: style: Variable 'ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/index-builder.c:802:70: style: Parameter 'out_fa' can be declared as pointer to const [constParameterPointer]
Rsubread/src/index-builder.c:891:14: style: Variable 'read_len' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-blc.c:43:15: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
Rsubread/src/input-blc.c:1660:8: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
Rsubread/src/input-blc.c:1652:13: note: outer condition: x1<4
Rsubread/src/input-blc.c:1660:8: note: opposite inner condition: x1==4
Rsubread/src/input-blc.c:396:26: style: Condition 'iCache_open_batch(cache_input)' is always false [knownConditionTrueFalse]
Rsubread/src/input-blc.c:396:26: note: Calling function 'iCache_open_batch' returns 0
Rsubread/src/input-blc.c:396:26: note: Condition 'iCache_open_batch(cache_input)' is always false
Rsubread/src/input-blc.c:841:9: style: Condition 'rv==0' is always true [knownConditionTrueFalse]
Rsubread/src/input-blc.c:837:18: note: Assuming that condition 'rv<0' is not redundant
Rsubread/src/input-blc.c:837:9: note: Assuming that condition 'rv>0' is not redundant
Rsubread/src/input-blc.c:841:9: note: Condition 'rv==0' is always true
Rsubread/src/input-blc.c:76:43: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/input-blc.c:69:21: note: Assuming allocation function fails
Rsubread/src/input-blc.c:69:21: note: Assignment 'fp=fopen(testfile_name,"rb")', assigned value is 0
Rsubread/src/input-blc.c:76:43: note: Null pointer dereference
Rsubread/src/input-blc.c:668:16: warning: If memory allocation fails, then there is a possible null pointer dereference: threads [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:661:30: note: Assuming allocation function fails
Rsubread/src/input-blc.c:661:30: note: Assignment 'threads=malloc(sizeof(pthread_t)*cache_input->all_threads)', assigned value is 0
Rsubread/src/input-blc.c:668:16: note: Null pointer dereference
Rsubread/src/input-blc.c:1002:4: warning: If memory allocation fails, then there is a possible null pointer dereference: entry [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1001:26: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1001:26: note: Assignment 'entry=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/input-blc.c:1002:4: note: Null pointer dereference
Rsubread/src/input-blc.c:1003:4: warning: If memory allocation fails, then there is a possible null pointer dereference: entry [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1001:26: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1001:26: note: Assignment 'entry=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/input-blc.c:1003:4: note: Null pointer dereference
Rsubread/src/input-blc.c:1004:4: warning: If memory allocation fails, then there is a possible null pointer dereference: entry [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1001:26: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1001:26: note: Assignment 'entry=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/input-blc.c:1004:4: note: Null pointer dereference
Rsubread/src/input-blc.c:1139:3: warning: If memory allocation fails, then there is a possible null pointer dereference: push_arr [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1134:28: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1134:28: note: Assignment 'push_arr=malloc(sizeof(char*)*3)', assigned value is 0
Rsubread/src/input-blc.c:1139:3: note: Null pointer dereference
Rsubread/src/input-blc.c:1140:3: warning: If memory allocation fails, then there is a possible null pointer dereference: push_arr [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1134:28: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1134:28: note: Assignment 'push_arr=malloc(sizeof(char*)*3)', assigned value is 0
Rsubread/src/input-blc.c:1140:3: note: Null pointer dereference
Rsubread/src/input-blc.c:1141:3: warning: If memory allocation fails, then there is a possible null pointer dereference: push_arr [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1134:28: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1134:28: note: Assignment 'push_arr=malloc(sizeof(char*)*3)', assigned value is 0
Rsubread/src/input-blc.c:1141:3: note: Null pointer dereference
Rsubread/src/input-blc.c:1461:10: warning: If resource allocation fails, then there is a possible null pointer dereference: result_supTab_fp [nullPointerOutOfResources]
Rsubread/src/input-blc.c:1460:33: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1460:33: note: Assignment 'result_supTab_fp=fopen(out_subTab_fn,"w")', assigned value is 0
Rsubread/src/input-blc.c:1461:10: note: Null pointer dereference
Rsubread/src/input-blc.c:1464:9: warning: If resource allocation fails, then there is a possible null pointer dereference: result_supTab_fp [nullPointerOutOfResources]
Rsubread/src/input-blc.c:1460:33: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1460:33: note: Assignment 'result_supTab_fp=fopen(out_subTab_fn,"w")', assigned value is 0
Rsubread/src/input-blc.c:1464:9: note: Null pointer dereference
Rsubread/src/input-blc.c:1540:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1688:27: note: Calling function 'scBAM_inner_fopen', 1st argument 'bam_input' value is 0
Rsubread/src/input-blc.c:1540:2: note: Null pointer dereference
Rsubread/src/input-blc.c:1540:37: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1688:27: note: Calling function 'scBAM_inner_fopen', 1st argument 'bam_input' value is 0
Rsubread/src/input-blc.c:1540:37: note: Null pointer dereference
Rsubread/src/input-blc.c:1540:65: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1688:27: note: Calling function 'scBAM_inner_fopen', 1st argument 'bam_input' value is 0
Rsubread/src/input-blc.c:1540:65: note: Null pointer dereference
Rsubread/src/input-blc.c:1541:6: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1688:27: note: Calling function 'scBAM_inner_fopen', 1st argument 'bam_input' value is 0
Rsubread/src/input-blc.c:1541:6: note: Null pointer dereference
Rsubread/src/input-blc.c:1627:48: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1261:5: note: Assuming condition is false
Rsubread/src/input-blc.c:1265:25: note: Calling function 'scBAM_next_read', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1627:48: note: Null pointer dereference
Rsubread/src/input-blc.c:1681:9: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1681:9: note: Null pointer dereference
Rsubread/src/input-blc.c:1683:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1683:3: note: Null pointer dereference
Rsubread/src/input-blc.c:1686:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
Rsubread/src/input-blc.c:1686:2: note: Null pointer dereference
Rsubread/src/input-blc.c:1745:3: warning: If memory allocation fails, then there is a possible null pointer dereference: files1 [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1736:25: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1736:25: note: Assignment 'files1=malloc(sizeof(char*)*256)', assigned value is 0
Rsubread/src/input-blc.c:1745:3: note: Null pointer dereference
Rsubread/src/input-blc.c:1747:3: warning: If memory allocation fails, then there is a possible null pointer dereference: files2 [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1737:25: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1737:25: note: Assignment 'files2=malloc(sizeof(char*)*256)', assigned value is 0
Rsubread/src/input-blc.c:1747:3: note: Null pointer dereference
Rsubread/src/input-blc.c:1750:3: warning: If memory allocation fails, then there is a possible null pointer dereference: files3 [nullPointerOutOfMemory]
Rsubread/src/input-blc.c:1738:25: note: Assuming allocation function fails
Rsubread/src/input-blc.c:1738:25: note: Assignment 'files3=malloc(sizeof(char*)*256)', assigned value is 0
Rsubread/src/input-blc.c:1750:3: note: Null pointer dereference
Rsubread/src/input-blc.c:665:25: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/input-blc.c:661:30: note: Assuming allocation function fails
Rsubread/src/input-blc.c:661:30: note: Assignment 'threads=malloc(sizeof(pthread_t)*cache_input->all_threads)', assigned value is 0
Rsubread/src/input-blc.c:665:25: note: Null pointer addition
Rsubread/src/input-blc.c:346:42: style:inconclusive: Function 'cacheBCL_go_chunk_end' argument 1 names different: declaration 'blc_input' definition 'cache_input'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:38:42: note: Function 'cacheBCL_go_chunk_end' argument 1 names different: declaration 'blc_input' definition 'cache_input'.
Rsubread/src/input-blc.c:346:42: note: Function 'cacheBCL_go_chunk_end' argument 1 names different: declaration 'blc_input' definition 'cache_input'.
Rsubread/src/input-blc.c:350:44: style:inconclusive: Function 'cacheBCL_go_chunk_start' argument 1 names different: declaration 'blc_input' definition 'cache_input'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:37:44: note: Function 'cacheBCL_go_chunk_start' argument 1 names different: declaration 'blc_input' definition 'cache_input'.
Rsubread/src/input-blc.c:350:44: note: Function 'cacheBCL_go_chunk_start' argument 1 names different: declaration 'blc_input' definition 'cache_input'.
Rsubread/src/input-blc.c:360:35: style:inconclusive: Function 'cacheBCL_close' argument 1 names different: declaration 'blc_input' definition 'cache_input'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:39:37: note: Function 'cacheBCL_close' argument 1 names different: declaration 'blc_input' definition 'cache_input'.
Rsubread/src/input-blc.c:360:35: note: Function 'cacheBCL_close' argument 1 names different: declaration 'blc_input' definition 'cache_input'.
Rsubread/src/input-blc.c:732:75: style:inconclusive: Function 'cacheBCL_next_readbin' argument 3 names different: declaration 'readbin' definition 'rbin'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:35:75: note: Function 'cacheBCL_next_readbin' argument 3 names different: declaration 'readbin' definition 'rbin'.
Rsubread/src/input-blc.c:732:75: note: Function 'cacheBCL_next_readbin' argument 3 names different: declaration 'readbin' definition 'rbin'.
Rsubread/src/input-blc.c:1405:31: style:inconclusive: Function 'cacheBCL_quality_test' argument 1 names different: declaration 'is_FASTQ_input' definition 'input_mode'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:56:31: note: Function 'cacheBCL_quality_test' argument 1 names different: declaration 'is_FASTQ_input' definition 'input_mode'.
Rsubread/src/input-blc.c:1405:31: note: Function 'cacheBCL_quality_test' argument 1 names different: declaration 'is_FASTQ_input' definition 'input_mode'.
Rsubread/src/input-blc.c:1626:55: style:inconclusive: Function 'scBAM_next_read' argument 2 names different: declaration 'readname' definition 'read_name'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:23:55: note: Function 'scBAM_next_read' argument 2 names different: declaration 'readname' definition 'read_name'.
Rsubread/src/input-blc.c:1626:55: note: Function 'scBAM_next_read' argument 2 names different: declaration 'readname' definition 'read_name'.
Rsubread/src/input-blc.c:1626:73: style:inconclusive: Function 'scBAM_next_read' argument 3 names different: declaration 'read' definition 'seq'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:23:73: note: Function 'scBAM_next_read' argument 3 names different: declaration 'read' definition 'seq'.
Rsubread/src/input-blc.c:1626:73: note: Function 'scBAM_next_read' argument 3 names different: declaration 'read' definition 'seq'.
Rsubread/src/input-blc.c:1675:56: style:inconclusive: Function 'input_scBAM_init' argument 2 names different: declaration 'bam_fname' definition 'bam_fnames'. [funcArgNamesDifferent]
Rsubread/src/input-blc.h:19:56: note: Function 'input_scBAM_init' argument 2 names different: declaration 'bam_fname' definition 'bam_fnames'.
Rsubread/src/input-blc.c:1675:56: note: Function 'input_scBAM_init' argument 2 names different: declaration 'bam_fname' definition 'bam_fnames'.
Rsubread/src/input-blc.c:488:21: style: Local variable 'ii' shadows outer variable [shadowVariable]
Rsubread/src/input-blc.c:434:29: note: Shadowed declaration
Rsubread/src/input-blc.c:488:21: note: Shadow variable
Rsubread/src/input-blc.c:1180:13: style: Local variable 'xx2' shadows outer variable [shadowVariable]
Rsubread/src/input-blc.c:1154:7: note: Shadowed declaration
Rsubread/src/input-blc.c:1180:13: note: Shadow variable
Rsubread/src/input-blc.c:84:15: style: Variable 'sec' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-blc.c:574:13: style: Variable 'np1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-blc.c:940:48: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:948:10: style: Variable 'gret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-blc.c:978:11: style: Variable 'sample_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-blc.c:1028:49: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1060:34: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1060:44: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1074:37: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1074:47: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1096:34: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1096:44: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1111:34: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1111:44: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1124:39: style: Parameter 'ky' can be declared as pointer to const. However it seems that 'iCache_write_supIdx_result' is a callback function, if 'ky' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/input-blc.c:1463:40: note: You might need to cast the function pointer here
Rsubread/src/input-blc.c:1124:39: note: Parameter 'ky' can be declared as pointer to const
Rsubread/src/input-blc.c:1124:49: style: Parameter 'va' can be declared as pointer to const. However it seems that 'iCache_write_supIdx_result' is a callback function, if 'va' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/input-blc.c:1463:40: note: You might need to cast the function pointer here
Rsubread/src/input-blc.c:1124:49: note: Parameter 'va' can be declared as pointer to const
Rsubread/src/input-blc.c:1148:36: style: Parameter 'cell_barcode_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1419:10: style: Variable 'bcbstr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-blc.c:1500:33: style: Parameter 'bam_input' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1588:64: style: Parameter 'pos' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1675:56: style: Parameter 'bam_fnames' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-blc.c:1678:9: style: Variable 'fnl1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-blc.c:1708:9: style: Variable 'lst' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-blc.c:573:21: style: Variable 'new_4digit' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-blc.c:580:22: style: Variable 'npos' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-blc.c:580:17: style: Variable 'npos' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-blc.c:1650:36: style: Variable 'tag_type' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-blc.c:1712:7: style: Variable 'lno' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-blc.c:1831:18: style: Variable 'write_ptr' is assigned a value that is never used. [unreadVariable]
Rsubread/src/gene-algorithms.c:1627:10: style: The if condition is the same as the previous if condition [duplicateCondition]
Rsubread/src/gene-algorithms.c:1623:10: note: First condition
Rsubread/src/gene-algorithms.c:1627:10: note: Second condition
Rsubread/src/gene-algorithms.c:1559:25: style: Condition 'path_i>=0' is always true [knownConditionTrueFalse]
Rsubread/src/gene-algorithms.c:1532:26: note: Assuming that condition 'path_i<0' is not redundant
Rsubread/src/gene-algorithms.c:1559:25: note: Condition 'path_i>=0' is always true
Rsubread/src/gene-algorithms.c:1570:7: style: Condition '!found' is always true [knownConditionTrueFalse]
Rsubread/src/gene-algorithms.c:1556:14: note: Assignment 'found=0', assigned value is 0
Rsubread/src/gene-algorithms.c:1570:7: note: Condition '!found' is always true
Rsubread/src/gene-algorithms.c:2266:28: style: Condition 'read_cursor<last_confirmed_read_pos' is always true [knownConditionTrueFalse]
Rsubread/src/gene-algorithms.c:2265:23: note: Assuming that condition 'read_cursor>=last_confirmed_read_pos' is not redundant
Rsubread/src/gene-algorithms.c:2266:28: note: Condition 'read_cursor<last_confirmed_read_pos' is always true
Rsubread/src/gene-algorithms.c:1008:16: warning: Possible null pointer dereference: indel_recorder [nullPointer]
Rsubread/src/gene-algorithms.c:1497:162: note: Calling function 'match_chro_indel', 8th argument 'NULL' value is 0
Rsubread/src/gene-algorithms.c:1008:16: note: Null pointer dereference
Rsubread/src/gene-algorithms.c:1010:30: warning: Possible null pointer dereference: indel_recorder [nullPointer]
Rsubread/src/gene-algorithms.c:1497:162: note: Calling function 'match_chro_indel', 8th argument 'NULL' value is 0
Rsubread/src/gene-algorithms.c:1010:30: note: Null pointer dereference
Rsubread/src/gene-algorithms.c:1011:24: warning: Possible null pointer dereference: indel_recorder [nullPointer]
Rsubread/src/gene-algorithms.c:1497:162: note: Calling function 'match_chro_indel', 8th argument 'NULL' value is 0
Rsubread/src/gene-algorithms.c:1011:24: note: Null pointer dereference
Rsubread/src/gene-algorithms.c:1013:7: warning: Possible null pointer dereference: indel_recorder [nullPointer]
Rsubread/src/gene-algorithms.c:1497:162: note: Calling function 'match_chro_indel', 8th argument 'NULL' value is 0
Rsubread/src/gene-algorithms.c:1013:7: note: Null pointer dereference
Rsubread/src/gene-algorithms.c:1352:10: warning: If memory allocation fails, then there is a possible null pointer dereference: read_name_mem [nullPointerOutOfMemory]
Rsubread/src/gene-algorithms.c:1351:32: note: Assuming allocation function fails
Rsubread/src/gene-algorithms.c:1351:32: note: Assignment 'read_name_mem=malloc(200)', assigned value is 0
Rsubread/src/gene-algorithms.c:1352:10: note: Null pointer dereference
Rsubread/src/gene-algorithms.c:910:15: style: Variable 'current_pos' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/gene-algorithms.c:904:16: note: current_pos is assigned
Rsubread/src/gene-algorithms.c:910:15: note: current_pos is overwritten
Rsubread/src/gene-algorithms.c:123:2: style: Statements following 'return' will never be executed. [unreachableCode]
Rsubread/src/gene-algorithms.c:2432:2: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
Rsubread/src/gene-algorithms.c:441:118: style:inconclusive: Function 'locate_gene_position_max' argument 5 names different: declaration 'head_cut' definition 'head_cut_length'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:36:118: note: Function 'locate_gene_position_max' argument 5 names different: declaration 'head_cut' definition 'head_cut_length'.
Rsubread/src/gene-algorithms.c:441:118: note: Function 'locate_gene_position_max' argument 5 names different: declaration 'head_cut' definition 'head_cut_length'.
Rsubread/src/gene-algorithms.c:441:141: style:inconclusive: Function 'locate_gene_position_max' argument 6 names different: declaration 'tail_cut' definition 'tail_cut_length'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:36:134: note: Function 'locate_gene_position_max' argument 6 names different: declaration 'tail_cut' definition 'tail_cut_length'.
Rsubread/src/gene-algorithms.c:441:141: note: Function 'locate_gene_position_max' argument 6 names different: declaration 'tail_cut' definition 'tail_cut_length'.
Rsubread/src/gene-algorithms.c:562:65: style:inconclusive: Function 'max_gene_vote' argument 3 names different: declaration 'query_id' definition 'query'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:49:65: note: Function 'max_gene_vote' argument 3 names different: declaration 'query_id' definition 'query'.
Rsubread/src/gene-algorithms.c:562:65: note: Function 'max_gene_vote' argument 3 names different: declaration 'query_id' definition 'query'.
Rsubread/src/gene-algorithms.c:667:306: style:inconclusive: Function 'find_and_explain_indel' argument 15 names different: declaration 'find_junctions' definition 'report_junction'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:100:305: note: Function 'find_and_explain_indel' argument 15 names different: declaration 'find_junctions' definition 'report_junction'.
Rsubread/src/gene-algorithms.c:667:306: note: Function 'find_and_explain_indel' argument 15 names different: declaration 'find_junctions' definition 'report_junction'.
Rsubread/src/gene-algorithms.c:784:297: style:inconclusive: Function 'explain_indel_in_middle' argument 14 names different: declaration 'find_junctions' definition 'report_junction'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:98:297: note: Function 'explain_indel_in_middle' argument 14 names different: declaration 'find_junctions' definition 'report_junction'.
Rsubread/src/gene-algorithms.c:784:297: note: Function 'explain_indel_in_middle' argument 14 names different: declaration 'find_junctions' definition 'report_junction'.
Rsubread/src/gene-algorithms.c:950:42: style:inconclusive: Function 'evaluate_piece' argument 2 names different: declaration 'chromosome' definition 'chron'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:52:42: note: Function 'evaluate_piece' argument 2 names different: declaration 'chromosome' definition 'chron'.
Rsubread/src/gene-algorithms.c:950:42: note: Function 'evaluate_piece' argument 2 names different: declaration 'chromosome' definition 'chron'.
Rsubread/src/gene-algorithms.c:950:85: style:inconclusive: Function 'evaluate_piece' argument 5 names different: declaration 'start_p' definition 'start_pos'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:52:90: note: Function 'evaluate_piece' argument 5 names different: declaration 'start_p' definition 'start_pos'.
Rsubread/src/gene-algorithms.c:950:85: note: Function 'evaluate_piece' argument 5 names different: declaration 'start_p' definition 'start_pos'.
Rsubread/src/gene-algorithms.c:950:100: style:inconclusive: Function 'evaluate_piece' argument 6 names different: declaration 'end_p' definition 'end_pos'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:52:103: note: Function 'evaluate_piece' argument 6 names different: declaration 'end_p' definition 'end_pos'.
Rsubread/src/gene-algorithms.c:950:100: note: Function 'evaluate_piece' argument 6 names different: declaration 'end_p' definition 'end_pos'.
Rsubread/src/gene-algorithms.c:1084:279: style:inconclusive: Function 'select_positions_array' argument 10 names different: declaration 'q_r1' definition 'qual_r1'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:74:278: note: Function 'select_positions_array' argument 10 names different: declaration 'q_r1' definition 'qual_r1'.
Rsubread/src/gene-algorithms.c:1084:279: note: Function 'select_positions_array' argument 10 names different: declaration 'q_r1' definition 'qual_r1'.
Rsubread/src/gene-algorithms.c:1084:311: style:inconclusive: Function 'select_positions_array' argument 11 names different: declaration 'q_r2' definition 'qual_r2'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:74:306: note: Function 'select_positions_array' argument 11 names different: declaration 'q_r2' definition 'qual_r2'.
Rsubread/src/gene-algorithms.c:1084:311: note: Function 'select_positions_array' argument 11 names different: declaration 'q_r2' definition 'qual_r2'.
Rsubread/src/gene-algorithms.c:1084:341: style:inconclusive: Function 'select_positions_array' argument 12 names different: declaration 'indel_rec_r1' definition 'r1_recorder'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:74:333: note: Function 'select_positions_array' argument 12 names different: declaration 'indel_rec_r1' definition 'r1_recorder'.
Rsubread/src/gene-algorithms.c:1084:341: note: Function 'select_positions_array' argument 12 names different: declaration 'indel_rec_r1' definition 'r1_recorder'.
Rsubread/src/gene-algorithms.c:1084:375: style:inconclusive: Function 'select_positions_array' argument 13 names different: declaration 'indel_rec_r2' definition 'r2_recorder'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:74:368: note: Function 'select_positions_array' argument 13 names different: declaration 'indel_rec_r2' definition 'r2_recorder'.
Rsubread/src/gene-algorithms.c:1084:375: note: Function 'select_positions_array' argument 13 names different: declaration 'indel_rec_r2' definition 'r2_recorder'.
Rsubread/src/gene-algorithms.c:1084:757: style:inconclusive: Function 'select_positions_array' argument 29 names different: declaration 'is_breakeven' definition 'is_break_even'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:74:751: note: Function 'select_positions_array' argument 29 names different: declaration 'is_breakeven' definition 'is_break_even'.
Rsubread/src/gene-algorithms.c:1084:757: note: Function 'select_positions_array' argument 29 names different: declaration 'is_breakeven' definition 'is_break_even'.
Rsubread/src/gene-algorithms.c:1097:400: style:inconclusive: Function 'select_positions' argument 12 names different: declaration 'max_pair_dist' definition 'max_pair_dest'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:71:399: note: Function 'select_positions' argument 12 names different: declaration 'max_pair_dist' definition 'max_pair_dest'.
Rsubread/src/gene-algorithms.c:1097:400: note: Function 'select_positions' argument 12 names different: declaration 'max_pair_dist' definition 'max_pair_dest'.
Rsubread/src/gene-algorithms.c:1097:428: style:inconclusive: Function 'select_positions' argument 13 names different: declaration 'min_pair_dist' definition 'min_pair_dest'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:71:427: note: Function 'select_positions' argument 13 names different: declaration 'min_pair_dist' definition 'min_pair_dest'.
Rsubread/src/gene-algorithms.c:1097:428: note: Function 'select_positions' argument 13 names different: declaration 'min_pair_dist' definition 'min_pair_dest'.
Rsubread/src/gene-algorithms.c:1097:476: style:inconclusive: Function 'select_positions' argument 16 names different: declaration 'is_negatve' definition 'is_negative_strand'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:71:476: note: Function 'select_positions' argument 16 names different: declaration 'is_negatve' definition 'is_negative_strand'.
Rsubread/src/gene-algorithms.c:1097:476: note: Function 'select_positions' argument 16 names different: declaration 'is_negatve' definition 'is_negative_strand'.
Rsubread/src/gene-algorithms.c:1600:172: style:inconclusive: Function 'window_indel_align' argument 8 names different: declaration 'begin_read_offset' definition 'init_read_offset'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:96:171: note: Function 'window_indel_align' argument 8 names different: declaration 'begin_read_offset' definition 'init_read_offset'.
Rsubread/src/gene-algorithms.c:1600:172: note: Function 'window_indel_align' argument 8 names different: declaration 'begin_read_offset' definition 'init_read_offset'.
Rsubread/src/gene-algorithms.c:1600:194: style:inconclusive: Function 'window_indel_align' argument 9 names different: declaration 'end_read_offset' definition 'shutdown_read_offset'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:96:194: note: Function 'window_indel_align' argument 9 names different: declaration 'end_read_offset' definition 'shutdown_read_offset'.
Rsubread/src/gene-algorithms.c:1600:194: note: Function 'window_indel_align' argument 9 names different: declaration 'end_read_offset' definition 'shutdown_read_offset'.
Rsubread/src/gene-algorithms.c:1710:167: style:inconclusive: Function 'dynamic_align' argument 8 names different: declaration 'begin_read_offset' definition 'init_read_offset'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:94:166: note: Function 'dynamic_align' argument 8 names different: declaration 'begin_read_offset' definition 'init_read_offset'.
Rsubread/src/gene-algorithms.c:1710:167: note: Function 'dynamic_align' argument 8 names different: declaration 'begin_read_offset' definition 'init_read_offset'.
Rsubread/src/gene-algorithms.c:1710:189: style:inconclusive: Function 'dynamic_align' argument 9 names different: declaration 'end_read_offset' definition 'shutdown_read_offset'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:94:189: note: Function 'dynamic_align' argument 9 names different: declaration 'end_read_offset' definition 'shutdown_read_offset'.
Rsubread/src/gene-algorithms.c:1710:189: note: Function 'dynamic_align' argument 9 names different: declaration 'end_read_offset' definition 'shutdown_read_offset'.
Rsubread/src/gene-algorithms.c:1710:219: style:inconclusive: Function 'dynamic_align' argument 10 names different: declaration 'dynamic_programming_short' definition 'table'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:94:214: note: Function 'dynamic_align' argument 10 names different: declaration 'dynamic_programming_short' definition 'table'.
Rsubread/src/gene-algorithms.c:1710:219: note: Function 'dynamic_align' argument 10 names different: declaration 'dynamic_programming_short' definition 'table'.
Rsubread/src/gene-algorithms.c:1710:237: style:inconclusive: Function 'dynamic_align' argument 11 names different: declaration 'dynamic_programming_char' definition 'table_mask'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:94:250: note: Function 'dynamic_align' argument 11 names different: declaration 'dynamic_programming_char' definition 'table_mask'.
Rsubread/src/gene-algorithms.c:1710:237: note: Function 'dynamic_align' argument 11 names different: declaration 'dynamic_programming_char' definition 'table_mask'.
Rsubread/src/gene-algorithms.c:1815:169: style:inconclusive: Function 'extend_covered_region' argument 8 names different: declaration 'match_req_5end' definition 'req_match_5end'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:102:169: note: Function 'extend_covered_region' argument 8 names different: declaration 'match_req_5end' definition 'req_match_5end'.
Rsubread/src/gene-algorithms.c:1815:169: note: Function 'extend_covered_region' argument 8 names different: declaration 'match_req_5end' definition 'req_match_5end'.
Rsubread/src/gene-algorithms.c:1815:190: style:inconclusive: Function 'extend_covered_region' argument 9 names different: declaration 'match_req_3end' definition 'req_match_3end'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:102:189: note: Function 'extend_covered_region' argument 9 names different: declaration 'match_req_3end' definition 'req_match_3end'.
Rsubread/src/gene-algorithms.c:1815:190: note: Function 'extend_covered_region' argument 9 names different: declaration 'match_req_3end' definition 'req_match_3end'.
Rsubread/src/gene-algorithms.c:1815:394: style:inconclusive: Function 'extend_covered_region' argument 18 names different: declaration 'qual_str' definition 'qual_txt'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:102:393: note: Function 'extend_covered_region' argument 18 names different: declaration 'qual_str' definition 'qual_txt'.
Rsubread/src/gene-algorithms.c:1815:394: note: Function 'extend_covered_region' argument 18 names different: declaration 'qual_str' definition 'qual_txt'.
Rsubread/src/gene-algorithms.c:1983:179: style:inconclusive: Function 'match_base_quality_cs' argument 8 names different: declaration 'all_MM' definition 'all_mismatched'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:136:179: note: Function 'match_base_quality_cs' argument 8 names different: declaration 'all_MM' definition 'all_mismatched'.
Rsubread/src/gene-algorithms.c:1983:179: note: Function 'match_base_quality_cs' argument 8 names different: declaration 'all_MM' definition 'all_mismatched'.
Rsubread/src/gene-algorithms.c:2012:193: style:inconclusive: Function 'match_base_quality' argument 9 names different: declaration 'all_MM' definition 'all_mismatched'. [funcArgNamesDifferent]
Rsubread/src/gene-algorithms.h:134:193: note: Function 'match_base_quality' argument 9 names different: declaration 'all_MM' definition 'all_mismatched'.
Rsubread/src/gene-algorithms.c:2012:193: note: Function 'match_base_quality' argument 9 names different: declaration 'all_MM' definition 'all_mismatched'.
Rsubread/src/gene-algorithms.c:863:10: style: Local variable 'vpos' shadows outer variable [shadowVariable]
Rsubread/src/gene-algorithms.c:835:7: note: Shadowed declaration
Rsubread/src/gene-algorithms.c:863:10: note: Shadow variable
Rsubread/src/gene-algorithms.c:872:11: style: Local variable 'vpos' shadows outer variable [shadowVariable]
Rsubread/src/gene-algorithms.c:835:7: note: Shadowed declaration
Rsubread/src/gene-algorithms.c:872:11: note: Shadow variable
Rsubread/src/gene-algorithms.c:892:8: style: Local variable 'vpos' shadows outer variable [shadowVariable]
Rsubread/src/gene-algorithms.c:835:7: note: Shadowed declaration
Rsubread/src/gene-algorithms.c:892:8: note: Shadow variable
Rsubread/src/gene-algorithms.c:130:33: style: Parameter 'qualityb' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:154:30: style: Parameter 'qualityb' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:171:36: style: Parameter 'qualityb' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:235:40: style: Parameter 'hint' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:235:81: style: Parameter 'internal_counter' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:419:72: style: Parameter 'chro_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:569:24: style: Variable 'vots' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gene-algorithms.c:655:36: style: Parameter 'allvote' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:655:158: style: Parameter 'max_indel_recorder' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:655:199: style: Parameter 'array_index' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:655:219: style: Parameter 'read_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:655:348: style: Parameter 'qual_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:950:27: style: Parameter 'piece_str' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:1156:17: style: Variable 'current_vote2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gene-algorithms.c:1983:69: style: Parameter 'read_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:2012:66: style: Parameter 'read_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:2012:102: style: Parameter 'qual_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/gene-algorithms.c:2442:21: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gene-algorithms.c:2443:21: style: Variable 'pv' can be declared as pointer to const [constVariablePointer]
Rsubread/src/gene-algorithms.c:2453:22: style: Variable 'p_nbv' can be declared as pointer to const [constVariablePointer]
Rsubread/src/long-hashtable.c:238:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable head_position [valueFlowBailoutIncompleteVar]
Rsubread/src/long-hashtable.c:256:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable head_position [valueFlowBailoutIncompleteVar]
Rsubread/src/gene-algorithms.c:1184:48: error: Uninitialized variable: minor_position[l] [legacyUninitvar]
Rsubread/src/gene-algorithms.c:793:22: style: Variable 'last_operation' is assigned a value that is never used. [unreadVariable]
Rsubread/src/gene-algorithms.c:907:10: style: Variable 'moves' is assigned a value that is never used. [unreadVariable]
Rsubread/src/gene-algorithms.c:909:18: style: Variable 'last_operation' is assigned a value that is never used. [unreadVariable]
Rsubread/src/gene-algorithms.c:910:15: style: Variable 'current_pos' is assigned a value that is never used. [unreadVariable]
Rsubread/src/long-hashtable.c:389:6: error: Common realloc mistake: 'ret' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/long-hashtable.c:368:22: warning: If memory allocation fails, then there is a possible null pointer dereference: arrtmp [nullPointerOutOfMemory]
Rsubread/src/long-hashtable.c:345:40: note: Assuming allocation function fails
Rsubread/src/long-hashtable.c:345:40: note: Assignment 'arrtmp=malloc(sizeof(struct lnhash_vote_record_t)*(items1+items2))', assigned value is 0
Rsubread/src/long-hashtable.c:368:22: note: Null pointer dereference
Rsubread/src/long-hashtable.c:117:3: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
Rsubread/src/long-hashtable.c:265:56: style:inconclusive: Function 'lnhash_query' argument 2 names different: declaration 'vote' definition 'votes'. [funcArgNamesDifferent]
Rsubread/src/long-hashtable.h:81:56: note: Function 'lnhash_query' argument 2 names different: declaration 'vote' definition 'votes'.
Rsubread/src/long-hashtable.c:265:56: note: Function 'lnhash_query' argument 2 names different: declaration 'vote' definition 'votes'.
Rsubread/src/long-hashtable.c:73:46: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/long-hashtable.c:327:25: style: Variable 'arr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/long-hashtable.c:351:26: style: Variable 'curr_pnt1_item' can be declared as pointer to const [constVariablePointer]
Rsubread/src/long-hashtable.c:352:26: style: Variable 'curr_pnt2_item' can be declared as pointer to const [constVariablePointer]
Rsubread/src/longread-mapping.c:77:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/longread-mapping.c:133:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/longread-mapping.c:230:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCK_REALTIME [valueFlowBailoutIncompleteVar]
Rsubread/src/mergeVCF.c:339:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/mergeVCF.c:369:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/mergeVCF.c:285:6: error: Common realloc mistake: 'output_list' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/mergeVCF.c:100:30: warning: If memory allocation fails, then there is a possible null pointer dereference: merge_tmp [nullPointerOutOfMemory]
Rsubread/src/mergeVCF.c:84:28: note: Assuming allocation function fails
Rsubread/src/mergeVCF.c:84:28: note: Assignment 'merge_tmp=malloc(sizeof(char*)*(items+items2))', assigned value is 0
Rsubread/src/mergeVCF.c:100:30: note: Null pointer dereference
Rsubread/src/mergeVCF.c:158:23: warning: If memory allocation fails, then there is a possible null pointer dereference: file_line [nullPointerOutOfMemory]
Rsubread/src/mergeVCF.c:128:27: note: Assuming allocation function fails
Rsubread/src/mergeVCF.c:128:27: note: Assignment 'file_line=malloc(3000)', assigned value is 0
Rsubread/src/mergeVCF.c:158:23: note: Null pointer dereference
Rsubread/src/mergeVCF.c:27:27: style: Parameter 'ky' can be declared as pointer to const [constParameterPointer]
Rsubread/src/mergeVCF.c:305:10: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:309:10: style: Variable 'id_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:310:10: style: Variable 'qual_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:311:10: style: Variable 'filter_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:313:10: style: Variable 'chro_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:314:10: style: Variable 'pos_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:316:10: style: Variable 'ref_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:317:10: style: Variable 'alt_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/mergeVCF.c:320:9: style: Variable 'brk' can be declared as pointer to const [constVariablePointer]
Rsubread/src/processExons.c:291:10: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf]
Rsubread/src/processExons.c:86:2: warning: If memory allocation fails, then there is a possible null pointer dereference: head [nullPointerOutOfMemory]
Rsubread/src/processExons.c:85:24: note: Assuming allocation function fails
Rsubread/src/processExons.c:85:9: note: Assignment 'head=(struct exon*)malloc(sizeof(*head))', assigned value is 0
Rsubread/src/processExons.c:86:2: note: Null pointer dereference
Rsubread/src/processExons.c:114:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_node [nullPointerOutOfMemory]
Rsubread/src/processExons.c:113:28: note: Assuming allocation function fails
Rsubread/src/processExons.c:113:13: note: Assignment 'new_node=(struct exon*)(malloc(sizeof(struct exon)))', assigned value is 0
Rsubread/src/processExons.c:114:2: note: Null pointer dereference
Rsubread/src/processExons.c:115:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_node [nullPointerOutOfMemory]
Rsubread/src/processExons.c:113:28: note: Assuming allocation function fails
Rsubread/src/processExons.c:113:13: note: Assignment 'new_node=(struct exon*)(malloc(sizeof(struct exon)))', assigned value is 0
Rsubread/src/processExons.c:115:2: note: Null pointer dereference
Rsubread/src/processExons.c:116:2: warning: If memory allocation fails, then there is a possible null pointer dereference: new_node [nullPointerOutOfMemory]
Rsubread/src/processExons.c:113:28: note: Assuming allocation function fails
Rsubread/src/processExons.c:113:13: note: Assignment 'new_node=(struct exon*)(malloc(sizeof(struct exon)))', assigned value is 0
Rsubread/src/processExons.c:116:2: note: Null pointer dereference
Rsubread/src/processExons.c:194:9: warning: If resource allocation fails, then there is a possible null pointer dereference: fexon [nullPointerOutOfResources]
Rsubread/src/processExons.c:174:15: note: Assuming allocation function fails
Rsubread/src/processExons.c:174:15: note: Assignment 'fexon=fopen(PEE_exon_file,"w")', assigned value is 0
Rsubread/src/processExons.c:194:9: note: Null pointer dereference
Rsubread/src/processExons.c:195:9: warning: If resource allocation fails, then there is a possible null pointer dereference: fgene [nullPointerOutOfResources]
Rsubread/src/processExons.c:175:15: note: Assuming allocation function fails
Rsubread/src/processExons.c:175:15: note: Assignment 'fgene=fopen(gene_file,"w")', assigned value is 0
Rsubread/src/processExons.c:195:9: note: Null pointer dereference
Rsubread/src/processExons.c:92:8: style: Variable 'chromosome' can be declared as pointer to const [constVariablePointer]
Rsubread/src/processExons.c:223:30: style: Parameter 'chr_id' can be declared as pointer to const [constParameterPointer]
Rsubread/src/processExons.c:105:63: warning: Uninitialized variable: gene_e [uninitvar]
Rsubread/src/processExons.c:99:14: note: Assuming condition is false
Rsubread/src/processExons.c:105:63: note: Uninitialized variable: gene_e
Rsubread/src/processExons.c:93:11: style: Variable 'gene' is assigned a value that is never used. [unreadVariable]
Rsubread/src/processExons.c:93:6: style: Variable 'gene' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:233:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:276:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:315:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:674:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:758:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:971:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:2205:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_offset [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:2399:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable zalloc [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:2531:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RLIMIT_NOFILE [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:2648:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable zalloc [valueFlowBailoutIncompleteVar]
Rsubread/src/propmapped.c:194:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/propmapped.c:451:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RLIMIT_NOFILE [valueFlowBailoutIncompleteVar]
Rsubread/src/propmapped.c:477:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/propmapped.c:389:20: warning: If memory allocation fails, then there is a possible null pointer dereference: read_name [nullPointerOutOfMemory]
Rsubread/src/propmapped.c:388:24: note: Assuming allocation function fails
Rsubread/src/propmapped.c:388:24: note: Assignment 'read_name=malloc((int)read_len+1)', assigned value is 0
Rsubread/src/propmapped.c:389:20: note: Null pointer dereference
Rsubread/src/propmapped.c:391:6: warning: If memory allocation fails, then there is a possible null pointer dereference: read_name [nullPointerOutOfMemory]
Rsubread/src/propmapped.c:388:24: note: Assuming allocation function fails
Rsubread/src/propmapped.c:388:24: note: Assignment 'read_name=malloc((int)read_len+1)', assigned value is 0
Rsubread/src/propmapped.c:390:14: note: Assuming condition is false
Rsubread/src/propmapped.c:391:6: note: Null pointer dereference
Rsubread/src/propmapped.c:475:9: warning: If memory allocation fails, then there is a possible null pointer dereference: context [nullPointerOutOfMemory]
Rsubread/src/propmapped.c:474:39: note: Assuming allocation function fails
Rsubread/src/propmapped.c:474:39: note: Assignment 'context=malloc(sizeof(struct propMapped_context))', assigned value is 0
Rsubread/src/propmapped.c:475:9: note: Null pointer dereference
Rsubread/src/propmapped.c:481:2: warning: If memory allocation fails, then there is a possible null pointer dereference: context [nullPointerOutOfMemory]
Rsubread/src/propmapped.c:474:39: note: Assuming allocation function fails
Rsubread/src/propmapped.c:474:39: note: Assignment 'context=malloc(sizeof(struct propMapped_context))', assigned value is 0
Rsubread/src/propmapped.c:481:2: note: Null pointer dereference
Rsubread/src/propmapped.c:145:10: style: Variable 'is_ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/propmapped.c:151:10: style: Variable 'flags_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/propmapped.c:265:41: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/propmapped.c:341:10: style: Variable 'is_ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/propmapped.c:348:10: style: Variable 'flags_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/longread-mapping.c:675:9: style: Condition '0&&LRMFIXLENstrcmp("R4",iteration_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/longread-mapping.c:692:9: style: Condition '0&&LRMFIXLENstrcmp("R4",iteration_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/longread-mapping.c:695:9: style: Condition '0&&LRMFIXLENstrcmp("R4",iteration_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/longread-mapping.c:1163:8: style: Condition '0&&LRMFIXLENstrcmp("R4",iteration_context->read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/qualityScores.c:305:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/longread-mapping.c:390:4: warning: If memory allocation fails, then there is a possible null pointer dereference: th_args [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:389:26: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:389:26: note: Assignment 'th_args=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/longread-mapping.c:390:4: note: Null pointer dereference
Rsubread/src/qualityScores.c:461:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/longread-mapping.c:391:4: warning: If memory allocation fails, then there is a possible null pointer dereference: th_args [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:389:26: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:389:26: note: Assignment 'th_args=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/longread-mapping.c:391:4: note: Null pointer dereference
Rsubread/src/qualityScores.c:517:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/longread-mapping.c:392:4: warning: If memory allocation fails, then there is a possible null pointer dereference: th_args [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:389:26: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:389:26: note: Assignment 'th_args=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/longread-mapping.c:392:4: note: Null pointer dereference
Rsubread/src/longread-mapping.c:561:64: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_locs [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:540:34: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:540:34: note: Assignment 'tmp_locs=malloc(sizeof(unsigned int)*(items+items2))', assigned value is 0
Rsubread/src/longread-mapping.c:561:64: note: Null pointer dereference
Rsubread/src/longread-mapping.c:562:61: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_subread_nos [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:541:41: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:541:41: note: Assignment 'tmp_subread_nos=malloc(sizeof(unsigned int)*(items+items2))', assigned value is 0
Rsubread/src/longread-mapping.c:562:61: note: Null pointer dereference
Rsubread/src/longread-mapping.c:563:63: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_votes [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:543:37: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:543:37: note: Assignment 'tmp_votes=malloc(sizeof(unsigned short)*(items+items2))', assigned value is 0
Rsubread/src/longread-mapping.c:563:63: note: Null pointer dereference
Rsubread/src/longread-mapping.c:564:68: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_negative [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:542:38: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:542:38: note: Assignment 'tmp_negative=malloc(sizeof(unsigned int)*(items+items2))', assigned value is 0
Rsubread/src/longread-mapping.c:564:68: note: Null pointer dereference
Rsubread/src/longread-mapping.c:618:2: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
Rsubread/src/longread-mapping.c:1184:59: note: Calling function 'LRMdo_dynamic_programming_read', 3rd argument 'iteration_context' value is 0
Rsubread/src/longread-mapping.c:1152:52: note: Calling function 'LRMcopy_longvotes_to_itr', 3rd argument 'iteration_context' value is 0
Rsubread/src/longread-mapping.c:618:2: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1146:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
Rsubread/src/longread-mapping.c:1184:59: note: Calling function 'LRMdo_dynamic_programming_read', 3rd argument 'iteration_context' value is 0
Rsubread/src/longread-mapping.c:1151:68: note: Calling function 'LRMreset_iteration_context_before_read', 3rd argument 'iteration_context' value is 0
Rsubread/src/longread-mapping.c:1146:5: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1153:35: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
Rsubread/src/longread-mapping.c:1184:59: note: Calling function 'LRMdo_dynamic_programming_read', 3rd argument 'iteration_context' value is 0
Rsubread/src/longread-mapping.c:1153:35: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1155:6: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
Rsubread/src/longread-mapping.c:1184:59: note: Calling function 'LRMdo_dynamic_programming_read', 3rd argument 'iteration_context' value is 0
Rsubread/src/longread-mapping.c:1155:6: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1155:53: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
Rsubread/src/longread-mapping.c:1184:59: note: Calling function 'LRMdo_dynamic_programming_read', 3rd argument 'iteration_context' value is 0
Rsubread/src/longread-mapping.c:1155:53: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1177:9: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1177:9: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1180:92: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1180:92: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1180:122: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1180:122: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1180:152: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1180:152: note: Null pointer dereference
Rsubread/src/longread-mapping.c:1186:6: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
Rsubread/src/longread-mapping.c:1186:6: note: Null pointer dereference
Rsubread/src/longread-mapping.c:977:33: style: Same value in both branches of ternary operator. [duplicateValueTernary]
Rsubread/src/longread-mapping.c:899:18: style: Redundant initialization for 'this_read_end'. The initialized value is overwritten before it is read. [redundantInitialization]
Rsubread/src/longread-mapping.c:858:22: note: this_read_end is initialized
Rsubread/src/longread-mapping.c:899:18: note: this_read_end is overwritten
Rsubread/src/longread-mapping.c:900:18: style: Redundant initialization for 'this_chro_pos'. The initialized value is overwritten before it is read. [redundantInitialization]
Rsubread/src/longread-mapping.c:859:28: note: this_chro_pos is initialized
Rsubread/src/longread-mapping.c:900:18: note: this_chro_pos is overwritten
Rsubread/src/longread-mapping.c:272:34: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:289:32: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:321:43: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:400:37: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:477:42: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:477:73: style: Parameter 'thread_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:477:119: style: Parameter 'iteration_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:511:32: style: Variable 'iteration_context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/longread-mapping.c:1045:65: style: Parameter 'context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/longread-mapping.c:1200:46: style: Parameter 'rname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/read-repair.c:12:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/read-repair.c:60:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/qualityScores.c:207:10: style: Condition '0&&qs_context->sam_end>0' is always false [knownConditionTrueFalse]
Rsubread/src/qualityScores.c:256:21: warning: If memory allocation fails, then there is a possible null pointer dereference: qual_buff [nullPointerOutOfMemory]
Rsubread/src/qualityScores.c:387:26: note: Assuming allocation function fails
Rsubread/src/qualityScores.c:387:26: note: Assignment 'linebuff=malloc(3000)', assigned value is 0
Rsubread/src/qualityScores.c:391:41: note: Calling function 'qs_next_qual', 2nd argument 'linebuff' value is 0
Rsubread/src/qualityScores.c:256:21: note: Null pointer dereference
Rsubread/src/qualityScores.c:257:5: warning: If memory allocation fails, then there is a possible null pointer dereference: qual_buff [nullPointerOutOfMemory]
Rsubread/src/qualityScores.c:387:26: note: Assuming allocation function fails
Rsubread/src/qualityScores.c:387:26: note: Assignment 'linebuff=malloc(3000)', assigned value is 0
Rsubread/src/qualityScores.c:391:41: note: Calling function 'qs_next_qual', 2nd argument 'linebuff' value is 0
Rsubread/src/qualityScores.c:257:5: note: Null pointer dereference
Rsubread/src/qualityScores.c:395:22: warning: If memory allocation fails, then there is a possible null pointer dereference: linebuff [nullPointerOutOfMemory]
Rsubread/src/qualityScores.c:387:26: note: Assuming allocation function fails
Rsubread/src/qualityScores.c:387:26: note: Assignment 'linebuff=malloc(3000)', assigned value is 0
Rsubread/src/qualityScores.c:393:7: note: Assuming condition is false
Rsubread/src/qualityScores.c:395:22: note: Null pointer dereference
Rsubread/src/qualityScores.c:396:7: warning: If memory allocation fails, then there is a possible null pointer dereference: linebuff [nullPointerOutOfMemory]
Rsubread/src/qualityScores.c:387:26: note: Assuming allocation function fails
Rsubread/src/qualityScores.c:387:26: note: Assignment 'linebuff=malloc(3000)', assigned value is 0
Rsubread/src/qualityScores.c:393:7: note: Assuming condition is false
Rsubread/src/qualityScores.c:396:7: note: Null pointer dereference
Rsubread/src/qualityScores.c:165:12: style: Variable 'retstr' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/qualityScores.c:160:12: note: retstr is assigned
Rsubread/src/qualityScores.c:165:12: note: retstr is overwritten
Rsubread/src/qualityScores.c:165:12: style: Variable 'retstr' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/qualityScores.c:162:12: note: retstr is assigned
Rsubread/src/qualityScores.c:165:12: note: retstr is overwritten
Rsubread/src/qualityScores.c:100:60: style: Parameter 'qual_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/qualityScores.c:141:10: style: Variable 'retstr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/qualityScores.c:192:11: style: Variable 'retstr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/qualityScores.c:200:13: style: Variable 'nstr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/qualityScores.c:287:30: style: Parameter 'strtype' can be declared as pointer to const [constParameterPointer]
Rsubread/src/qualityScores.c:349:41: style: Parameter 'offset_pt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/qualityScores.c:349:63: style: Parameter 'size' can be declared as pointer to const [constParameterPointer]
Rsubread/src/qualityScores.c:349:75: style: Parameter 'sam_whichend' can be declared as pointer to const [constParameterPointer]
Rsubread/src/removeDupReads.c:296:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/removeDupReads.c:353:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/removeDupReads.c:56:3: error: Common realloc mistake: 'read_selection_list' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/removeDupReads.c:176:10: style: Variable 'opret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sam2bed.c:54:8: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/sam2bed.c:57:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/sam2bed.c:58:8: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/sam2bed.c:60:25: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/sam2bed.c:62:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/sam2bed.c:50:16: warning: Either the condition 'line' is redundant or there is possible null pointer dereference: line. [nullPointerRedundantCheck]
Rsubread/src/sam2bed.c:74:7: note: Assuming that condition 'line' is not redundant
Rsubread/src/sam2bed.c:50:16: note: Null pointer dereference
Rsubread/src/sam2bed.c:50:39: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
Rsubread/src/sam2bed.c:36:11: note: Assuming allocation function fails
Rsubread/src/sam2bed.c:36:11: note: Assignment 'fp=fopen(argv[3],"r")', assigned value is 0
Rsubread/src/sam2bed.c:50:39: note: Null pointer dereference
Rsubread/src/sam2bed.c:25:28: style: Parameter 'argv' can be declared as const array [constParameter]
Rsubread/src/sam2bed.c:41:10: style: Variable 'chr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sam2bed.c:41:16: style: Variable 'tok' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:303:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/readSummary.c:4544:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/readSummary.c:4845:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/readSummary.c:4937:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUBREAD_VERSION [valueFlowBailoutIncompleteVar]
Rsubread/src/readSummary.c:6451:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/sambam-file.c:275:39: error: Array 'ret->bam_chro_table[xk1].chro_name[200]' accessed at index 255, which is out of bounds. [arrayIndexOutOfBounds]
Rsubread/src/sambam-file.c:271:24: note: Assignment 'ref_readin_len=(ref_name_len)>(256-1)?(256-1):(ref_name_len)', assigned value is 255
Rsubread/src/sambam-file.c:275:39: note: Array index out of bounds
Rsubread/src/sambam-file.c:1217:2: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/sambam-file.c:1223:2: warning: Return value of function deflate() is not used. [ignoredReturnValue]
Rsubread/src/sambam-file.c:2390:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/sambam-file.c:2594:4: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/sambam-file.c:2600:4: warning: Return value of function deflate() is not used. [ignoredReturnValue]
Rsubread/src/sambam-file.c:452:19: style: Condition 'CDATA_READING<CDATA_LEN' is always false [knownConditionTrueFalse]
Rsubread/src/sambam-file.c:449:21: note: CDATA_READING is assigned '(CDATA_LEN)>(buffer_length)?(buffer_length):(CDATA_LEN)' here.
Rsubread/src/sambam-file.c:451:11: note: Assuming condition is false
Rsubread/src/sambam-file.c:452:19: note: Condition 'CDATA_READING<CDATA_LEN' is always false
Rsubread/src/sambam-file.c:672:26: style: Condition 'elemtype=='s'' is always false [knownConditionTrueFalse]
Rsubread/src/sambam-file.c:714:26: style: Condition 'tagtype=='s'' is always false [knownConditionTrueFalse]
Rsubread/src/sambam-file.c:2087:17: style: Condition 'this_size<2' is always false [knownConditionTrueFalse]
Rsubread/src/sambam-file.c:2086:20: note: Assignment 'this_size=(350)>(writer->sorted_batch_id-merge_i)?(writer->sorted_batch_id-merge_i):(350)', assigned value is 350
Rsubread/src/sambam-file.c:2087:17: note: Condition 'this_size<2' is always false
Rsubread/src/sambam-file.c:90:15: error: Resource leak: fp [resourceLeak]
Rsubread/src/sambam-file.c:111:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:111:9: note: Null pointer dereference
Rsubread/src/sambam-file.c:112:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:112:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:116:3: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:116:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:117:7: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:117:7: note: Null pointer dereference
Rsubread/src/sambam-file.c:143:3: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:143:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:144:6: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:144:6: note: Null pointer dereference
Rsubread/src/sambam-file.c:149:34: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:144:21: note: Assuming condition is false
Rsubread/src/sambam-file.c:149:34: note: Null pointer dereference
Rsubread/src/sambam-file.c:150:35: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:110:43: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:110:22: note: Assignment 'ret=(struct SamBam_FILE*)malloc(sizeof(struct SamBam_FILE))', assigned value is 0
Rsubread/src/sambam-file.c:144:21: note: Assuming condition is false
Rsubread/src/sambam-file.c:150:35: note: Null pointer dereference
Rsubread/src/sambam-file.c:1357:28: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: header_text [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:1414:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1414:27: note: Assignment 'line_buf=malloc(1000)', assigned value is 0
Rsubread/src/sambam-file.c:1416:36: note: Calling function 'SamBam_writer_add_header', 2nd argument 'line_buf' value is 0
Rsubread/src/sambam-file.c:1357:28: note: Null pointer dereference
Rsubread/src/sambam-file.c:1367:87: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: header_text [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:1414:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1414:27: note: Assignment 'line_buf=malloc(1000)', assigned value is 0
Rsubread/src/sambam-file.c:1416:36: note: Calling function 'SamBam_writer_add_header', 2nd argument 'line_buf' value is 0
Rsubread/src/sambam-file.c:1367:87: note: Null pointer dereference
Rsubread/src/sambam-file.c:1407:9: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_name_space [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:1406:33: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1406:33: note: Assignment 'chro_name_space=malloc(strlen(chro_name)+1)', assigned value is 0
Rsubread/src/sambam-file.c:1407:9: note: Null pointer dereference
Rsubread/src/sambam-file.c:1415:12: warning: If memory allocation fails, then there is a possible null pointer dereference: line_buf [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:1414:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1414:27: note: Assignment 'line_buf=malloc(1000)', assigned value is 0
Rsubread/src/sambam-file.c:1415:12: note: Null pointer dereference
Rsubread/src/sambam-file.c:1631:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:1630:21: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1630:21: note: Assignment 'ret=malloc(end_pos-start_pos+1)', assigned value is 0
Rsubread/src/sambam-file.c:1631:9: note: Null pointer dereference
Rsubread/src/sambam-file.c:1632:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:1630:21: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1630:21: note: Assignment 'ret=malloc(end_pos-start_pos+1)', assigned value is 0
Rsubread/src/sambam-file.c:1632:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:1850:10: warning: If memory allocation fails, then there is a possible null pointer dereference: key_binpos [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:1849:29: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1849:29: note: Assignment 'key_binpos=malloc(12)', assigned value is 0
Rsubread/src/sambam-file.c:1850:10: note: Null pointer dereference
Rsubread/src/sambam-file.c:2100:5: warning: If memory allocation fails, then there is a possible null pointer dereference: current_min_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2094:49: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2094:49: note: Assignment 'current_min_fps=malloc(sizeof(unsigned long long)*this_size)', assigned value is 0
Rsubread/src/sambam-file.c:2100:5: note: Null pointer dereference
Rsubread/src/sambam-file.c:2103:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sb_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2093:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2093:27: note: Assignment 'sb_fps=malloc(sizeof(FILE*)*this_size)', assigned value is 0
Rsubread/src/sambam-file.c:2103:5: note: Null pointer dereference
Rsubread/src/sambam-file.c:2104:5: warning: If memory allocation fails, then there is a possible null pointer dereference: current_min_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2094:49: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2094:49: note: Assignment 'current_min_fps=malloc(sizeof(unsigned long long)*this_size)', assigned value is 0
Rsubread/src/sambam-file.c:2104:5: note: Null pointer dereference
Rsubread/src/sambam-file.c:2104:66: warning: If memory allocation fails, then there is a possible null pointer dereference: sb_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2093:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2093:27: note: Assignment 'sb_fps=malloc(sizeof(FILE*)*this_size)', assigned value is 0
Rsubread/src/sambam-file.c:2104:66: note: Null pointer dereference
Rsubread/src/sambam-file.c:2105:8: warning: If memory allocation fails, then there is a possible null pointer dereference: current_min_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2094:49: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2094:49: note: Assignment 'current_min_fps=malloc(sizeof(unsigned long long)*this_size)', assigned value is 0
Rsubread/src/sambam-file.c:2105:8: note: Null pointer dereference
Rsubread/src/sambam-file.c:2105:56: warning: If memory allocation fails, then there is a possible null pointer dereference: current_min_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2094:49: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2094:49: note: Assignment 'current_min_fps=malloc(sizeof(unsigned long long)*this_size)', assigned value is 0
Rsubread/src/sambam-file.c:2105:56: note: Null pointer dereference
Rsubread/src/sambam-file.c:2173:3: warning: If memory allocation fails, then there is a possible null pointer dereference: ll [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2172:26: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2172:26: note: Assignment 'll=malloc(sizeof(long long)*2)', assigned value is 0
Rsubread/src/sambam-file.c:2173:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2174:3: warning: If memory allocation fails, then there is a possible null pointer dereference: ll [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2172:26: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2172:26: note: Assignment 'll=malloc(sizeof(long long)*2)', assigned value is 0
Rsubread/src/sambam-file.c:2174:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2358:3: warning: If memory allocation fails, then there is a possible null pointer dereference: current_min_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2350:47: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2350:47: note: Assignment 'current_min_fps=malloc(sizeof(unsigned long long)*writer->sorted_batch_id)', assigned value is 0
Rsubread/src/sambam-file.c:2358:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2361:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sb_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2349:25: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2349:25: note: Assignment 'sb_fps=malloc(sizeof(FILE*)*writer->sorted_batch_id)', assigned value is 0
Rsubread/src/sambam-file.c:2361:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2362:6: warning: If memory allocation fails, then there is a possible null pointer dereference: sb_fps [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2349:25: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2349:25: note: Assignment 'sb_fps=malloc(sizeof(FILE*)*writer->sorted_batch_id)', assigned value is 0
Rsubread/src/sambam-file.c:2362:6: note: Null pointer dereference
Rsubread/src/sambam-file.c:2396:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thparam [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2395:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2395:27: note: Assignment 'thparam=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/sambam-file.c:2396:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2397:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thparam [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2395:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2395:27: note: Assignment 'thparam=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/sambam-file.c:2397:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2398:3: warning: If memory allocation fails, then there is a possible null pointer dereference: thparam [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2395:27: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2395:27: note: Assignment 'thparam=malloc(sizeof(void*)*3)', assigned value is 0
Rsubread/src/sambam-file.c:2398:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2515:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2514:56: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2514:56: note: Assignment 'ret=malloc(sizeof(struct simple_bam_writer_index_per_chro))', assigned value is 0
Rsubread/src/sambam-file.c:2515:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:2516:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2514:56: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2514:56: note: Assignment 'ret=malloc(sizeof(struct simple_bam_writer_index_per_chro))', assigned value is 0
Rsubread/src/sambam-file.c:2516:36: note: Null pointer dereference
Rsubread/src/sambam-file.c:2517:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2514:56: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2514:56: note: Assignment 'ret=malloc(sizeof(struct simple_bam_writer_index_per_chro))', assigned value is 0
Rsubread/src/sambam-file.c:2517:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:2518:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2514:56: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2514:56: note: Assignment 'ret=malloc(sizeof(struct simple_bam_writer_index_per_chro))', assigned value is 0
Rsubread/src/sambam-file.c:2518:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:2587:28: warning: If memory allocation fails, then there is a possible null pointer dereference: writer [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2613:31: note: Calling function 'simple_bam_write', 3rd argument 'ret' value is 0
Rsubread/src/sambam-file.c:2587:28: note: Null pointer dereference
Rsubread/src/sambam-file.c:2588:10: warning: If memory allocation fails, then there is a possible null pointer dereference: writer [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2613:31: note: Calling function 'simple_bam_write', 3rd argument 'ret' value is 0
Rsubread/src/sambam-file.c:2588:10: note: Null pointer dereference
Rsubread/src/sambam-file.c:2588:24: warning: If memory allocation fails, then there is a possible null pointer dereference: writer [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2613:31: note: Calling function 'simple_bam_write', 3rd argument 'ret' value is 0
Rsubread/src/sambam-file.c:2588:24: note: Null pointer dereference
Rsubread/src/sambam-file.c:2590:3: warning: If memory allocation fails, then there is a possible null pointer dereference: writer [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2613:31: note: Calling function 'simple_bam_write', 3rd argument 'ret' value is 0
Rsubread/src/sambam-file.c:2590:3: note: Null pointer dereference
Rsubread/src/sambam-file.c:2611:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2611:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:2612:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2612:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:2618:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2618:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:2619:24: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2619:24: note: Null pointer dereference
Rsubread/src/sambam-file.c:2620:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2620:2: note: Null pointer dereference
Rsubread/src/sambam-file.c:2621:36: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
Rsubread/src/sambam-file.c:2621:36: note: Null pointer dereference
Rsubread/src/sambam-file.c:1851:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/sambam-file.c:1849:29: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1849:29: note: Assignment 'key_binpos=malloc(12)', assigned value is 0
Rsubread/src/sambam-file.c:1851:20: note: Null pointer addition
Rsubread/src/sambam-file.c:1852:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/sambam-file.c:1849:29: note: Assuming allocation function fails
Rsubread/src/sambam-file.c:1849:29: note: Assignment 'key_binpos=malloc(12)', assigned value is 0
Rsubread/src/sambam-file.c:1852:20: note: Null pointer addition
Rsubread/src/sambam-file.c:1045:7: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/sambam-file.c:1039:7: note: ret is assigned
Rsubread/src/sambam-file.c:1045:7: note: ret is overwritten
Rsubread/src/sambam-file.c:2024:8: style: Variable 'rlen' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/sambam-file.c:2023:8: note: rlen is assigned
Rsubread/src/sambam-file.c:2024:8: note: rlen is overwritten
Rsubread/src/sambam-file.c:2239:33: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
Rsubread/src/sambam-file.c:999:78: style:inconclusive: Function 'PBum_load_header' argument 3 names different: declaration 'remainder_read_data' definition 'remainder_reads_data'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:179:78: note: Function 'PBum_load_header' argument 3 names different: declaration 'remainder_read_data' definition 'remainder_reads_data'.
Rsubread/src/sambam-file.c:999:78: note: Function 'PBum_load_header' argument 3 names different: declaration 'remainder_read_data' definition 'remainder_reads_data'.
Rsubread/src/sambam-file.c:999:107: style:inconclusive: Function 'PBum_load_header' argument 4 names different: declaration 'remainder_read_data_len' definition 'remainder_reads_data_len'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:179:105: note: Function 'PBum_load_header' argument 4 names different: declaration 'remainder_read_data_len' definition 'remainder_reads_data_len'.
Rsubread/src/sambam-file.c:999:107: note: Function 'PBum_load_header' argument 4 names different: declaration 'remainder_read_data_len' definition 'remainder_reads_data_len'.
Rsubread/src/sambam-file.c:1095:110: style:inconclusive: Function 'SamBam_writer_create' argument 5 names different: declaration 'is_tmp_BAM' definition 'is_temp_BAM_file'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:216:110: note: Function 'SamBam_writer_create' argument 5 names different: declaration 'is_tmp_BAM' definition 'is_temp_BAM_file'.
Rsubread/src/sambam-file.c:1095:110: note: Function 'SamBam_writer_create' argument 5 names different: declaration 'is_tmp_BAM' definition 'is_temp_BAM_file'.
Rsubread/src/sambam-file.c:1399:106: style:inconclusive: Function 'SamBam_writer_add_chromosome' argument 4 names different: declaration 'add_header_too' definition 'add_header'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:222:106: note: Function 'SamBam_writer_add_chromosome' argument 4 names different: declaration 'add_header_too' definition 'add_header'.
Rsubread/src/sambam-file.c:1399:106: note: Function 'SamBam_writer_add_chromosome' argument 4 names different: declaration 'add_header_too' definition 'add_header'.
Rsubread/src/sambam-file.c:1605:53: style:inconclusive: Function 'duplicate_TAB_record_field' argument 2 names different: declaration 'fld_no' definition 'fno'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:250:52: note: Function 'duplicate_TAB_record_field' argument 2 names different: declaration 'fld_no' definition 'fno'.
Rsubread/src/sambam-file.c:1605:53: note: Function 'duplicate_TAB_record_field' argument 2 names different: declaration 'fld_no' definition 'fno'.
Rsubread/src/sambam-file.c:1605:62: style:inconclusive: Function 'duplicate_TAB_record_field' argument 3 names different: declaration 'toend' definition 'to_end'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:250:64: note: Function 'duplicate_TAB_record_field' argument 3 names different: declaration 'toend' definition 'to_end'.
Rsubread/src/sambam-file.c:1605:62: note: Function 'duplicate_TAB_record_field' argument 3 names different: declaration 'toend' definition 'to_end'.
Rsubread/src/sambam-file.c:1666:90: style:inconclusive: Function 'SamBam_writer_add_read_line' argument 4 names different: declaration 'commitable' definition 'committable'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:249:90: note: Function 'SamBam_writer_add_read_line' argument 4 names different: declaration 'commitable' definition 'committable'.
Rsubread/src/sambam-file.c:1666:90: note: Function 'SamBam_writer_add_read_line' argument 4 names different: declaration 'commitable' definition 'committable'.
Rsubread/src/sambam-file.c:1702:56: style:inconclusive: Function 'SamBam_writer_add_read' argument 2 names different: declaration 'threadno' definition 'thread_no'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:230:56: note: Function 'SamBam_writer_add_read' argument 2 names different: declaration 'threadno' definition 'thread_no'.
Rsubread/src/sambam-file.c:1702:56: note: Function 'SamBam_writer_add_read' argument 2 names different: declaration 'threadno' definition 'thread_no'.
Rsubread/src/sambam-file.c:1702:222: style:inconclusive: Function 'SamBam_writer_add_read' argument 10 names different: declaration 'next_chro_pos' definition 'next_chro_position'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:230:221: note: Function 'SamBam_writer_add_read' argument 10 names different: declaration 'next_chro_pos' definition 'next_chro_position'.
Rsubread/src/sambam-file.c:1702:222: note: Function 'SamBam_writer_add_read' argument 10 names different: declaration 'next_chro_pos' definition 'next_chro_position'.
Rsubread/src/sambam-file.c:1702:337: style:inconclusive: Function 'SamBam_writer_add_read' argument 16 names different: declaration 'can_submit' definition 'committable'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:230:331: note: Function 'SamBam_writer_add_read' argument 16 names different: declaration 'can_submit' definition 'committable'.
Rsubread/src/sambam-file.c:1702:337: note: Function 'SamBam_writer_add_read' argument 16 names different: declaration 'can_submit' definition 'committable'.
Rsubread/src/sambam-file.c:1797:34: style:inconclusive: Function 'SamBam_unzip' argument 2 names different: declaration 'out_max_len' definition 'outlen'. [funcArgNamesDifferent]
Rsubread/src/sambam-file.h:236:34: note: Function 'SamBam_unzip' argument 2 names different: declaration 'out_max_len' definition 'outlen'.
Rsubread/src/sambam-file.c:1797:34: note: Function 'SamBam_unzip' argument 2 names different: declaration 'out_max_len' definition 'outlen'.
Rsubread/src/sambam-file.c:98:10: style: Variable 'is_ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:108:35: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:962:9: style: Variable 'chro_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:963:9: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:973:9: style: Variable 'mate_chro_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:1095:135: style: Parameter 'tmpfname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1184:34: style: Parameter 'dat' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1399:65: style: Parameter 'chro_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1424:34: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1458:29: style: Parameter 'read_txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1605:42: style: Parameter 'rline' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1636:78: style: Parameter 'rbin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1702:74: style: Parameter 'read_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1702:112: style: Parameter 'chro_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1702:193: style: Parameter 'next_chro_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1702:295: style: Parameter 'qual_text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:1831:79: style: Parameter 'me' can be declared as pointer to const. However it seems that 'SamBam_writer_sort_buff_one_compare' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/sambam-file.c:1859:33: note: You might need to cast the function pointer here
Rsubread/src/sambam-file.c:1831:79: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/sambam-file.c:1832:23: style: Variable 'Lv' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:1832:35: style: Variable 'Rv' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:1865:9: style: Variable 'binpos' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:2159:74: style: Parameter 'me' can be declared as pointer to const. However it seems that 'SamBam_writer_merge_chunks_compare' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/sambam-file.c:2179:23: note: You might need to cast the function pointer here
Rsubread/src/sambam-file.c:2159:74: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/sambam-file.c:2160:14: style: Variable 'lL' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:2161:14: style: Variable 'lR' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:2180:14: style: Variable 'll0' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sambam-file.c:2497:30: style: Parameter 'dat' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:2573:73: style: Parameter 'obuf' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:2609:46: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sambam-file.c:2591:7: portability: 'bin' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/sambam-file.c:1787:56: warning: Uninitialized variable: additional_bin [uninitvar]
Rsubread/src/sambam-file.c:1716:5: note: Assuming condition is false
Rsubread/src/sambam-file.c:1787:56: note: Uninitialized variable: additional_bin
Rsubread/src/sambam-file.c:2580:9: warning: Uninitialized variable: obuf [uninitvar]
Rsubread/src/sambam-file.c:2602:46: note: Calling function 'simple_bam_write_compressed_block', 2nd argument 'obuf' value is <Uninit>
Rsubread/src/sambam-file.c:2580:9: note: Uninitialized variable: obuf
Rsubread/src/sambam-file.c:124:23: style: Variable 'nchold' is assigned a value that is never used. [unreadVariable]
Rsubread/src/sambam-file.c:1004:125: style: Variable 'bam_is_broken' is assigned a value that is never used. [unreadVariable]
Rsubread/src/sambam-file.c:1896:25: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
Rsubread/src/sambam-file.c:2024:8: style: Variable 'rlen' is assigned a value that is never used. [unreadVariable]
Rsubread/src/seek-zlib.c:524:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/seek-zlib.c:581:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/seek-zlib.c:637:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
Rsubread/src/seek-zlib.c:676:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/seek-zlib.c:323:23: style: The if condition is the same as the previous if condition [duplicateCondition]
Rsubread/src/seek-zlib.c:318:23: note: First condition
Rsubread/src/seek-zlib.c:323:23: note: Second condition
Rsubread/src/seek-zlib.c:476:7: style: Condition 'buff' is always true [knownConditionTrueFalse]
Rsubread/src/seek-zlib.c:227:5: error: Common realloc mistake: 'arr' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/seek-zlib.c:307:5: error: Common realloc mistake: 'out_txt' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/seek-zlib.c:431:47: style:inconclusive: Function 'seekgz_gets' argument 2 names different: declaration 'buf' definition 'buff'. [funcArgNamesDifferent]
Rsubread/src/seek-zlib.h:49:47: note: Function 'seekgz_gets' argument 2 names different: declaration 'buf' definition 'buff'.
Rsubread/src/seek-zlib.c:431:47: note: Function 'seekgz_gets' argument 2 names different: declaration 'buf' definition 'buff'.
Rsubread/src/seek-zlib.c:431:57: style:inconclusive: Function 'seekgz_gets' argument 3 names different: declaration 'buf_size' definition 'buff_len'. [funcArgNamesDifferent]
Rsubread/src/seek-zlib.h:49:56: note: Function 'seekgz_gets' argument 3 names different: declaration 'buf_size' definition 'buff_len'.
Rsubread/src/seek-zlib.c:431:57: note: Function 'seekgz_gets' argument 3 names different: declaration 'buf_size' definition 'buff_len'.
Rsubread/src/seek-zlib.c:704:81: style:inconclusive: Function 'parallel_gzip_zip_texts' argument 3 names different: declaration 'for_eof_marker' definition 'eof_marker'. [funcArgNamesDifferent]
Rsubread/src/seek-zlib.h:39:81: note: Function 'parallel_gzip_zip_texts' argument 3 names different: declaration 'for_eof_marker' definition 'eof_marker'.
Rsubread/src/seek-zlib.c:704:81: note: Function 'parallel_gzip_zip_texts' argument 3 names different: declaration 'for_eof_marker' definition 'eof_marker'.
Rsubread/src/seek-zlib.c:16:29: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:151:37: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:153:35: style: Variable 'curr_block' can be declared as pointer to const [constVariablePointer]
Rsubread/src/seek-zlib.c:237:66: style: Parameter 'txt' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:314:11: style: Variable 'old_next_in' can be declared as pointer to const [constVariablePointer]
Rsubread/src/seek-zlib.c:614:11: style: Variable 'retc' can be declared as pointer to const [constVariablePointer]
Rsubread/src/seek-zlib.c:620:10: style: Variable 'rets' can be declared as pointer to const [constVariablePointer]
Rsubread/src/seek-zlib.c:657:71: style: Parameter 'output_filename' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:686:66: style: Parameter 'pzwtr' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:686:80: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:697:61: style: Parameter 'pzwtr' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:697:75: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
Rsubread/src/seek-zlib.c:704:55: style: Parameter 'pzwtr' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:881:32: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][21], which is out of bounds. [arrayIndexOutOfBoundsCond]
Rsubread/src/sorted-hashtable.c:877:18: note: Assuming that condition 'toli<7*3' is not redundant
Rsubread/src/sorted-hashtable.c:881:32: note: Array index out of bounds
Rsubread/src/sorted-hashtable.c:882:32: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][22], which is out of bounds. [arrayIndexOutOfBoundsCond]
Rsubread/src/sorted-hashtable.c:877:18: note: Assuming that condition 'toli<7*3' is not redundant
Rsubread/src/sorted-hashtable.c:882:32: note: Array index out of bounds
Rsubread/src/sorted-hashtable.c:1057:31: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][21], which is out of bounds. [arrayIndexOutOfBoundsCond]
Rsubread/src/sorted-hashtable.c:1053:17: note: Assuming that condition 'toli<7*3' is not redundant
Rsubread/src/sorted-hashtable.c:1057:31: note: Array index out of bounds
Rsubread/src/sorted-hashtable.c:1058:31: warning: Either the condition 'toli<7*3' is redundant or the array 'vote->indel_recorder[30][24][21]' is accessed at index vote->indel_recorder[*][*][22], which is out of bounds. [arrayIndexOutOfBoundsCond]
Rsubread/src/sorted-hashtable.c:1053:17: note: Assuming that condition 'toli<7*3' is not redundant
Rsubread/src/sorted-hashtable.c:1058:31: note: Array index out of bounds
Rsubread/src/sorted-hashtable.c:1151:11: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
Rsubread/src/sorted-hashtable.c:1861:9: style: Condition '1||real_key>=0xffffff00' is always true [knownConditionTrueFalse]
Rsubread/src/sorted-hashtable.c:142:4: error: Memory leak: new_item_values [memleak]
Rsubread/src/sorted-hashtable.c:231:11: warning: If memory allocation fails, then there is a possible null pointer dereference: memory_sizes [nullPointerOutOfMemory]
Rsubread/src/sorted-hashtable.c:230:40: note: Assuming allocation function fails
Rsubread/src/sorted-hashtable.c:230:40: note: Assignment 'memory_sizes=malloc(sizeof(int)*the_table->buckets_number)', assigned value is 0
Rsubread/src/sorted-hashtable.c:231:11: note: Null pointer dereference
Rsubread/src/sorted-hashtable.c:248:34: warning: If memory allocation fails, then there is a possible null pointer dereference: memory_sizes [nullPointerOutOfMemory]
Rsubread/src/sorted-hashtable.c:230:40: note: Assuming allocation function fails
Rsubread/src/sorted-hashtable.c:230:40: note: Assignment 'memory_sizes=malloc(sizeof(int)*the_table->buckets_number)', assigned value is 0
Rsubread/src/sorted-hashtable.c:248:34: note: Null pointer dereference
Rsubread/src/sorted-hashtable.c:1477:10: warning: If memory allocation fails, then there is a possible null pointer dereference: bucket_bytes [nullPointerOutOfMemory]
Rsubread/src/sorted-hashtable.c:1476:39: note: Assuming allocation function fails
Rsubread/src/sorted-hashtable.c:1476:39: note: Assignment 'bucket_bytes=malloc(sizeof(int)*(64*1024))', assigned value is 0
Rsubread/src/sorted-hashtable.c:1477:10: note: Null pointer dereference
Rsubread/src/sorted-hashtable.c:180:38: style: Same expression on both sides of '||'. [duplicateExpression]
Rsubread/src/sorted-hashtable.c:42:48: style:inconclusive: Function 'calculate_buckets_by_size' argument 1 names different: declaration 'exp_size' definition 'expected_size'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:106:47: note: Function 'calculate_buckets_by_size' argument 1 names different: declaration 'exp_size' definition 'expected_size'.
Rsubread/src/sorted-hashtable.c:42:48: note: Function 'calculate_buckets_by_size' argument 1 names different: declaration 'exp_size' definition 'expected_size'.
Rsubread/src/sorted-hashtable.c:42:67: style:inconclusive: Function 'calculate_buckets_by_size' argument 2 names different: declaration 'version' definition 'version_number'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:106:61: note: Function 'calculate_buckets_by_size' argument 2 names different: declaration 'version' definition 'version_number'.
Rsubread/src/sorted-hashtable.c:42:67: note: Function 'calculate_buckets_by_size' argument 2 names different: declaration 'version' definition 'version_number'.
Rsubread/src/sorted-hashtable.c:42:87: style:inconclusive: Function 'calculate_buckets_by_size' argument 3 names different: declaration 'is_small_tab' definition 'is_small_table'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:106:74: note: Function 'calculate_buckets_by_size' argument 3 names different: declaration 'is_small_tab' definition 'is_small_table'.
Rsubread/src/sorted-hashtable.c:42:87: note: Function 'calculate_buckets_by_size' argument 3 names different: declaration 'is_small_tab' definition 'is_small_table'.
Rsubread/src/sorted-hashtable.c:77:111: style:inconclusive: Function 'gehash_create_ex' argument 5 names different: declaration 'GENE_SLIDING_STEP' definition 'index_gap'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:47:111: note: Function 'gehash_create_ex' argument 5 names different: declaration 'GENE_SLIDING_STEP' definition 'index_gap'.
Rsubread/src/sorted-hashtable.c:77:111: note: Function 'gehash_create_ex' argument 5 names different: declaration 'GENE_SLIDING_STEP' definition 'index_gap'.
Rsubread/src/sorted-hashtable.c:305:91: style:inconclusive: Function 'gehash_insert_limited' argument 4 names different: declaration 'max_key_occurance' definition 'limit'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:54:91: note: Function 'gehash_insert_limited' argument 4 names different: declaration 'max_key_occurance' definition 'limit'.
Rsubread/src/sorted-hashtable.c:305:91: note: Function 'gehash_insert_limited' argument 4 names different: declaration 'max_key_occurance' definition 'limit'.
Rsubread/src/sorted-hashtable.c:305:102: style:inconclusive: Function 'gehash_insert_limited' argument 5 names different: declaration 'prob_replace' definition 'replace_prob'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:54:114: note: Function 'gehash_insert_limited' argument 5 names different: declaration 'prob_replace' definition 'replace_prob'.
Rsubread/src/sorted-hashtable.c:305:102: note: Function 'gehash_insert_limited' argument 5 names different: declaration 'prob_replace' definition 'replace_prob'.
Rsubread/src/sorted-hashtable.c:515:55: style:inconclusive: Function 'gehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:70:55: note: Function 'gehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/sorted-hashtable.c:515:55: note: Function 'gehash_go_q' argument 2 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/sorted-hashtable.c:937:55: style:inconclusive: Function 'gehash_go_X' argument 2 names different: declaration 'key' definition 'raw_key'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:71:55: note: Function 'gehash_go_X' argument 2 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/sorted-hashtable.c:937:55: note: Function 'gehash_go_X' argument 2 names different: declaration 'key' definition 'raw_key'.
Rsubread/src/sorted-hashtable.c:937:249: style:inconclusive: Function 'gehash_go_X' argument 12 names different: declaration 'shift_indel_locations' definition 'shift_indel_locs'. [funcArgNamesDifferent]
Rsubread/src/sorted-hashtable.h:71:244: note: Function 'gehash_go_X' argument 12 names different: declaration 'shift_indel_locations' definition 'shift_indel_locs'.
Rsubread/src/sorted-hashtable.c:937:249: note: Function 'gehash_go_X' argument 12 names different: declaration 'shift_indel_locations' definition 'shift_indel_locs'.
Rsubread/src/sorted-hashtable.c:200:94: style: Parameter 'bucket_sizes' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:515:31: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:525:18: style: Variable 'current_keys' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:638:21: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:759:10: style: Variable 'current_keys' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:821:27: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:937:31: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:950:9: style: Variable 'current_keys' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:1001:26: style: Variable 'dat' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:1144:73: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1175:29: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1179:24: style: Variable 'endkp' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:1205:24: style: Variable 'endkp' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:1229:30: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1234:24: style: Variable 'endkp' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:1304:34: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1304:79: style: Parameter 'data_result' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1310:38: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1660:63: style: Parameter 'option_value' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1668:42: style: Parameter 'the_table' can be declared as pointer to const [constParameterPointer]
Rsubread/src/sorted-hashtable.c:1727:26: style: Variable 'current_bucket' can be declared as pointer to const [constVariablePointer]
Rsubread/src/sorted-hashtable.c:203:15: style: Variable 'is_fault' is assigned a value that is never used. [unreadVariable]
Rsubread/src/sorted-hashtable.c:378:25: style: Variable 'base_to_change' is assigned a value that is never used. [unreadVariable]
Rsubread/src/sorted-hashtable.c:460:25: style: Variable 'base_to_change' is assigned a value that is never used. [unreadVariable]
Rsubread/src/sublog.c:87:5: style: Condition 'to_remove_ESC' is always true [knownConditionTrueFalse]
Rsubread/src/sublog.c:80:22: note: Assignment 'to_remove_ESC=1', assigned value is 1
Rsubread/src/sublog.c:87:5: note: Condition 'to_remove_ESC' is always true
Rsubread/src/sublog.c:122:5: style: Condition 'to_remove_ESC' is always true [knownConditionTrueFalse]
Rsubread/src/sublog.c:117:22: note: Assignment 'to_remove_ESC=1', assigned value is 1
Rsubread/src/sublog.c:122:5: note: Condition 'to_remove_ESC' is always true
Rsubread/src/sublog.c:42:7: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: txt [nullPointerOutOfMemory]
Rsubread/src/sublog.c:124:22: note: Assuming allocation function fails
Rsubread/src/sublog.c:124:22: note: Assignment 'vsbuf=malloc(1200)', assigned value is 0
Rsubread/src/sublog.c:127:22: note: Calling function 'remove_ESC_effects', 1st argument 'vsbuf' value is 0
Rsubread/src/sublog.c:42:7: note: Null pointer dereference
Rsubread/src/sublog.c:43:23: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: txt [nullPointerOutOfMemory]
Rsubread/src/sublog.c:124:22: note: Assuming allocation function fails
Rsubread/src/sublog.c:124:22: note: Assignment 'vsbuf=malloc(1200)', assigned value is 0
Rsubread/src/sublog.c:127:22: note: Calling function 'remove_ESC_effects', 1st argument 'vsbuf' value is 0
Rsubread/src/sublog.c:42:6: note: Assuming condition is false
Rsubread/src/sublog.c:43:23: note: Null pointer dereference
Rsubread/src/sublog.c:128:13: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: vsbuf [nullPointerOutOfMemory]
Rsubread/src/sublog.c:124:22: note: Assuming allocation function fails
Rsubread/src/sublog.c:124:22: note: Assignment 'vsbuf=malloc(1200)', assigned value is 0
Rsubread/src/sublog.c:128:13: note: Null pointer dereference
Rsubread/src/sublog.c:78:36: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
Rsubread/src/sublog.c:115:36: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
Rsubread/src/input-files.c:5259:2: error: Address of local auto-variable assigned to a function parameter. [autoVariables]
Rsubread/src/input-files.c:5260:2: error: Address of local auto-variable assigned to a function parameter. [autoVariables]
Rsubread/src/input-files.c:2221:19: error: Array 'this_gene_name[128]' accessed at index 1199, which is out of bounds. [arrayIndexOutOfBounds]
Rsubread/src/input-files.c:2222:18: error: Array 'this_gene_name[128]' accessed at index 1200, which is out of bounds. [arrayIndexOutOfBounds]
Rsubread/src/input-files.c:2220:4: note: After for loop, i has value 1200
Rsubread/src/input-files.c:2222:18: note: Array index out of bounds
Rsubread/src/input-files.c:2274:3: warning:inconclusive: The buffer 'old_gene_name' may not be null-terminated after the call to strncpy(). [terminateStrncpy]
Rsubread/src/input-files.c:2405:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:2467:3: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:2654:3: warning: Return value of function inflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:4756:4: warning: Return value of function deflate() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:4769:4: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:4776:4: warning: Return value of function deflate() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:4850:2: warning: Return value of function inflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:4858:2: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:5510:2: warning: Return value of function inflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/input-files.c:67:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/input-files.c:2351:19: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
Rsubread/src/input-files.c:4539:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/input-files.c:5184:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/input-files.c:5343:19: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/input-files.c:5474:19: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
Rsubread/src/input-files.c:5855:6: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/input-files.c:6006:7: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
Rsubread/src/tx-unique.c:388:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar]
Rsubread/src/input-files.c:2065:14: style: Condition '0&&FIXLENstrcmp("SRR768163.14829906",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/input-files.c:2068:14: style: Condition '0&&strcmp(chro,"chr12")==0' is always false [knownConditionTrueFalse]
Rsubread/src/input-files.c:4432:10: style: Condition 'nch=='\t'' is always false [knownConditionTrueFalse]
Rsubread/src/input-files.c:4431:10: note: Assuming that condition 'nch<0x20' is not redundant
Rsubread/src/input-files.c:4432:10: note: Condition 'nch=='\t'' is always false
Rsubread/src/input-files.c:4744:22: style: Condition 'binlen-written<1' is always false [knownConditionTrueFalse]
Rsubread/src/input-files.c:4815:12: note: Assuming that condition 'binlen<1' is not redundant
Rsubread/src/input-files.c:4741:41: note: Assignment 'written=0', assigned value is 0
Rsubread/src/input-files.c:4744:22: note: Condition 'binlen-written<1' is always false
Rsubread/src/input-files.c:5524:18: style: Condition 'disk_is_full' is always false [knownConditionTrueFalse]
Rsubread/src/input-files.c:5515:22: note: Assignment 'disk_is_full=0', assigned value is 0
Rsubread/src/input-files.c:5524:18: note: Condition 'disk_is_full' is always false
Rsubread/src/input-files.c:5921:7: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/input-files.c:6011:7: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/input-files.c:2981:7: error: Common realloc mistake: 'header_txt' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:4183:5: error: Common realloc mistake: 'orphant_fps' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:4266:6: error: Common realloc mistake: 'orphant_fps' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:5541:4: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:5561:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:5568:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:5586:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:5594:5: error: Common realloc mistake: 'bin_buffer' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/input-files.c:75:9: warning: If memory allocation fails, then there is a possible null pointer dereference: new_ret [nullPointerOutOfMemory]
Rsubread/src/input-files.c:74:25: note: Assuming allocation function fails
Rsubread/src/input-files.c:74:25: note: Assignment 'new_ret=malloc(new_size)', assigned value is 0
Rsubread/src/input-files.c:75:9: note: Null pointer dereference
Rsubread/src/input-files.c:84:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/input-files.c:83:21: note: Assuming allocation function fails
Rsubread/src/input-files.c:83:21: note: Assignment 'ret=malloc(ilen+1)', assigned value is 0
Rsubread/src/input-files.c:84:9: note: Null pointer dereference
Rsubread/src/input-files.c:85:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/input-files.c:83:21: note: Assuming allocation function fails
Rsubread/src/input-files.c:83:21: note: Assignment 'ret=malloc(ilen+1)', assigned value is 0
Rsubread/src/input-files.c:85:2: note: Null pointer dereference
Rsubread/src/input-files.c:601:25: warning: If memory allocation fails, then there is a possible null pointer dereference: out_buf [nullPointerOutOfMemory]
Rsubread/src/input-files.c:586:27: note: Assuming allocation function fails
Rsubread/src/input-files.c:586:27: note: Assignment 'out_buf=malloc(2000)', assigned value is 0
Rsubread/src/input-files.c:593:15: note: Assuming condition is false
Rsubread/src/input-files.c:601:25: note: Null pointer dereference
Rsubread/src/input-files.c:1717:11: warning: If memory allocation fails, then there is a possible null pointer dereference: token_1 [nullPointerOutOfMemory]
Rsubread/src/input-files.c:1716:27: note: Assuming allocation function fails
Rsubread/src/input-files.c:1716:27: note: Assignment 'token_1=malloc(token_len+1)', assigned value is 0
Rsubread/src/input-files.c:1717:11: note: Null pointer dereference
Rsubread/src/input-files.c:1727:10: warning: If memory allocation fails, then there is a possible null pointer dereference: token_2 [nullPointerOutOfMemory]
Rsubread/src/input-files.c:1726:26: note: Assuming allocation function fails
Rsubread/src/input-files.c:1726:26: note: Assignment 'token_2=malloc(token_len+1)', assigned value is 0
Rsubread/src/input-files.c:1727:10: note: Null pointer dereference
Rsubread/src/input-files.c:1735:11: warning: If memory allocation fails, then there is a possible null pointer dereference: ins_seq_2 [nullPointerOutOfMemory]
Rsubread/src/input-files.c:1734:29: note: Assuming allocation function fails
Rsubread/src/input-files.c:1734:29: note: Assignment 'ins_seq_2=malloc(-indels)', assigned value is 0
Rsubread/src/input-files.c:1735:11: note: Null pointer dereference
Rsubread/src/input-files.c:1797:6: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: linebuf [nullPointerOutOfMemory]
Rsubread/src/input-files.c:1789:25: note: Assuming allocation function fails
Rsubread/src/input-files.c:1789:25: note: Assignment 'linebuf=malloc(3000)', assigned value is 0
Rsubread/src/input-files.c:1796:12: note: Assuming condition is false
Rsubread/src/input-files.c:1797:6: note: Null pointer dereference
Rsubread/src/input-files.c:1876:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fns [nullPointerOutOfMemory]
Rsubread/src/input-files.c:1875:21: note: Assuming allocation function fails
Rsubread/src/input-files.c:1875:21: note: Assignment 'fns=malloc(200)', assigned value is 0
Rsubread/src/input-files.c:1876:2: note: Null pointer dereference
Rsubread/src/input-files.c:1878:27: warning: If memory allocation fails, then there is a possible null pointer dereference: fns [nullPointerOutOfMemory]
Rsubread/src/input-files.c:1875:21: note: Assuming allocation function fails
Rsubread/src/input-files.c:1875:21: note: Assignment 'fns=malloc(200)', assigned value is 0
Rsubread/src/input-files.c:1878:27: note: Null pointer dereference
Rsubread/src/input-files.c:2488:10: warning: If memory allocation fails, then there is a possible null pointer dereference: BAM_compressed [nullPointerOutOfMemory]
Rsubread/src/input-files.c:2447:32: note: Assuming allocation function fails
Rsubread/src/input-files.c:2447:32: note: Assignment 'BAM_compressed=malloc(65536)', assigned value is 0
Rsubread/src/input-files.c:2488:10: note: Null pointer dereference
Rsubread/src/input-files.c:3025:14: warning: If memory allocation fails, then there is a possible null pointer dereference: margin_data [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3023:34: note: Assuming allocation function fails
Rsubread/src/input-files.c:3023:34: note: Assignment 'margin_data=malloc(thread_context->input_buff_BIN_used-thread_context->input_buff_BIN_ptr+4)', assigned value is 0
Rsubread/src/input-files.c:3025:14: note: Null pointer dereference
Rsubread/src/input-files.c:3164:9: warning: If memory allocation fails, then there is a possible null pointer dereference: header_sec [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3162:28: note: Assuming allocation function fails
Rsubread/src/input-files.c:3162:28: note: Assignment 'header_sec=malloc(reflen+20)', assigned value is 0
Rsubread/src/input-files.c:3164:9: note: Null pointer dereference
Rsubread/src/input-files.c:3174:10: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_ref [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3173:26: note: Assuming allocation function fails
Rsubread/src/input-files.c:3173:26: note: Assignment 'mem_ref=malloc(reflen+1)', assigned value is 0
Rsubread/src/input-files.c:3174:10: note: Null pointer dereference
Rsubread/src/input-files.c:3175:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_ref [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3173:26: note: Assuming allocation function fails
Rsubread/src/input-files.c:3173:26: note: Assignment 'mem_ref=malloc(reflen+1)', assigned value is 0
Rsubread/src/input-files.c:3175:3: note: Null pointer dereference
Rsubread/src/input-files.c:3843:10: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_name [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3842:27: note: Assuming allocation function fails
Rsubread/src/input-files.c:3842:27: note: Assignment 'mem_name=malloc(read_name_len+1)', assigned value is 0
Rsubread/src/input-files.c:3843:10: note: Null pointer dereference
Rsubread/src/input-files.c:3844:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_name [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3842:27: note: Assuming allocation function fails
Rsubread/src/input-files.c:3842:27: note: Assignment 'mem_name=malloc(read_name_len+1)', assigned value is 0
Rsubread/src/input-files.c:3844:3: note: Null pointer dereference
Rsubread/src/input-files.c:3847:10: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_bin [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3846:26: note: Assuming allocation function fails
Rsubread/src/input-files.c:3846:26: note: Assignment 'mem_bin=malloc(bin_len)', assigned value is 0
Rsubread/src/input-files.c:3847:10: note: Null pointer dereference
Rsubread/src/input-files.c:3860:9: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_bin [nullPointerOutOfMemory]
Rsubread/src/input-files.c:3859:25: note: Assuming allocation function fails
Rsubread/src/input-files.c:3859:25: note: Assignment 'mem_bin=malloc(bin_len)', assigned value is 0
Rsubread/src/input-files.c:3860:9: note: Null pointer dereference
Rsubread/src/input-files.c:4168:3: warning: If memory allocation fails, then there is a possible null pointer dereference: orphant_fps [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4159:30: note: Assuming allocation function fails
Rsubread/src/input-files.c:4159:30: note: Assignment 'orphant_fps=malloc(sizeof(FILE*)*orphant_fp_size)', assigned value is 0
Rsubread/src/input-files.c:4164:11: note: Assuming condition is false
Rsubread/src/input-files.c:4168:3: note: Null pointer dereference
Rsubread/src/input-files.c:4274:9: warning: If memory allocation fails, then there is a possible null pointer dereference: names [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4273:23: note: Assuming allocation function fails
Rsubread/src/input-files.c:4273:23: note: Assignment 'names=malloc(orphant_fp_no*max_name_len)', assigned value is 0
Rsubread/src/input-files.c:4274:9: note: Null pointer dereference
Rsubread/src/input-files.c:4359:4: warning: If memory allocation fails, then there is a possible null pointer dereference: name_list [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4351:20: note: Assuming allocation function fails
Rsubread/src/input-files.c:4351:20: note: Assignment 'name_list=malloc(sizeof(char*)*thread_context->orphant_table->numOfElements)', assigned value is 0
Rsubread/src/input-files.c:4359:4: note: Null pointer dereference
Rsubread/src/input-files.c:4360:4: warning: If memory allocation fails, then there is a possible null pointer dereference: bin_list [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4352:20: note: Assuming allocation function fails
Rsubread/src/input-files.c:4352:20: note: Assignment 'bin_list=malloc(sizeof(char*)*thread_context->orphant_table->numOfElements)', assigned value is 0
Rsubread/src/input-files.c:4360:4: note: Null pointer dereference
Rsubread/src/input-files.c:4504:10: warning: If memory allocation fails, then there is a possible null pointer dereference: margin_data [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4503:30: note: Assuming allocation function fails
Rsubread/src/input-files.c:4503:30: note: Assignment 'margin_data=malloc(save_start_pos+4)', assigned value is 0
Rsubread/src/input-files.c:4504:10: note: Null pointer dereference
Rsubread/src/input-files.c:4607:10: warning: If memory allocation fails, then there is a possible null pointer dereference: tb [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4606:21: note: Assuming allocation function fails
Rsubread/src/input-files.c:4606:21: note: Assignment 'tb=malloc(Elen+Slen)', assigned value is 0
Rsubread/src/input-files.c:4607:10: note: Null pointer dereference
Rsubread/src/input-files.c:4646:3: warning: If memory allocation fails, then there is a possible null pointer dereference: init_params [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4644:31: note: Assuming allocation function fails
Rsubread/src/input-files.c:4644:31: note: Assignment 'init_params=malloc(sizeof(void*)*2)', assigned value is 0
Rsubread/src/input-files.c:4646:3: note: Null pointer dereference
Rsubread/src/input-files.c:4647:3: warning: If memory allocation fails, then there is a possible null pointer dereference: init_params [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4644:31: note: Assuming allocation function fails
Rsubread/src/input-files.c:4644:31: note: Assignment 'init_params=malloc(sizeof(void*)*2)', assigned value is 0
Rsubread/src/input-files.c:4647:3: note: Null pointer dereference
Rsubread/src/input-files.c:4667:5: warning: If memory allocation fails, then there is a possible null pointer dereference: init_params [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4665:33: note: Assuming allocation function fails
Rsubread/src/input-files.c:4665:33: note: Assignment 'init_params=malloc(sizeof(void*)*2)', assigned value is 0
Rsubread/src/input-files.c:4667:5: note: Null pointer dereference
Rsubread/src/input-files.c:4668:5: warning: If memory allocation fails, then there is a possible null pointer dereference: init_params [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4665:33: note: Assuming allocation function fails
Rsubread/src/input-files.c:4665:33: note: Assignment 'init_params=malloc(sizeof(void*)*2)', assigned value is 0
Rsubread/src/input-files.c:4668:5: note: Null pointer dereference
Rsubread/src/input-files.c:4807:27: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_buf [nullPointerOutOfMemory]
Rsubread/src/input-files.c:4746:26: note: Assuming allocation function fails
Rsubread/src/input-files.c:4746:26: note: Assignment 'bam_buf=malloc(70000)', assigned value is 0
Rsubread/src/input-files.c:4807:27: note: Null pointer dereference
Rsubread/src/input-files.c:5245:3: warning: If memory allocation fails, then there is a possible null pointer dereference: init_params [nullPointerOutOfMemory]
Rsubread/src/input-files.c:5243:31: note: Assuming allocation function fails
Rsubread/src/input-files.c:5243:31: note: Assignment 'init_params=malloc(sizeof(void*)*2)', assigned value is 0
Rsubread/src/input-files.c:5245:3: note: Null pointer dereference
Rsubread/src/input-files.c:5246:3: warning: If memory allocation fails, then there is a possible null pointer dereference: init_params [nullPointerOutOfMemory]
Rsubread/src/input-files.c:5243:31: note: Assuming allocation function fails
Rsubread/src/input-files.c:5243:31: note: Assignment 'init_params=malloc(sizeof(void*)*2)', assigned value is 0
Rsubread/src/input-files.c:5246:3: note: Null pointer dereference
Rsubread/src/input-files.c:5410:12: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_contig_name [nullPointerOutOfMemory]
Rsubread/src/input-files.c:5409:36: note: Assuming allocation function fails
Rsubread/src/input-files.c:5409:36: note: Assignment 'mem_contig_name=malloc(sqname_len)', assigned value is 0
Rsubread/src/input-files.c:5410:12: note: Null pointer dereference
Rsubread/src/input-files.c:5759:18: warning: If memory allocation fails, then there is a possible null pointer dereference: read_name [nullPointerOutOfMemory]
Rsubread/src/input-files.c:5758:24: note: Assuming allocation function fails
Rsubread/src/input-files.c:5758:24: note: Assignment 'read_name=malloc(read_name_len+1)', assigned value is 0
Rsubread/src/input-files.c:5759:18: note: Null pointer dereference
Rsubread/src/input-files.c:5761:6: warning: If memory allocation fails, then there is a possible null pointer dereference: read_name [nullPointerOutOfMemory]
Rsubread/src/input-files.c:5758:24: note: Assuming allocation function fails
Rsubread/src/input-files.c:5758:24: note: Assignment 'read_name=malloc(read_name_len+1)', assigned value is 0
Rsubread/src/input-files.c:5760:12: note: Assuming condition is false
Rsubread/src/input-files.c:5761:6: note: Null pointer dereference
Rsubread/src/input-files.c:5771:18: warning: If memory allocation fails, then there is a possible null pointer dereference: new_line_mem [nullPointerOutOfMemory]
Rsubread/src/input-files.c:5770:34: note: Assuming allocation function fails
Rsubread/src/input-files.c:5770:34: note: Assignment 'new_line_mem=malloc(read_len+1)', assigned value is 0
Rsubread/src/input-files.c:5771:18: note: Null pointer dereference
Rsubread/src/input-files.c:5774:6: warning: If memory allocation fails, then there is a possible null pointer dereference: new_line_mem [nullPointerOutOfMemory]
Rsubread/src/input-files.c:5770:34: note: Assuming allocation function fails
Rsubread/src/input-files.c:5770:34: note: Assignment 'new_line_mem=malloc(read_len+1)', assigned value is 0
Rsubread/src/input-files.c:5772:12: note: Assuming condition is false
Rsubread/src/input-files.c:5774:6: note: Null pointer dereference
Rsubread/src/input-files.c:3026:25: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/input-files.c:3023:34: note: Assuming allocation function fails
Rsubread/src/input-files.c:3023:34: note: Assignment 'margin_data=malloc(thread_context->input_buff_BIN_used-thread_context->input_buff_BIN_ptr+4)', assigned value is 0
Rsubread/src/input-files.c:3026:25: note: Null pointer addition
Rsubread/src/input-files.c:3072:38: warning: Either the condition 'NULL==line_ptr' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
Rsubread/src/input-files.c:3071:13: note: Assuming that condition 'NULL==line_ptr' is not redundant
Rsubread/src/input-files.c:3072:38: note: Null pointer subtraction
Rsubread/src/input-files.c:3165:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/input-files.c:3162:28: note: Assuming allocation function fails
Rsubread/src/input-files.c:3162:28: note: Assignment 'header_sec=malloc(reflen+20)', assigned value is 0
Rsubread/src/input-files.c:3165:20: note: Null pointer addition
Rsubread/src/input-files.c:3166:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/input-files.c:3162:28: note: Assuming allocation function fails
Rsubread/src/input-files.c:3162:28: note: Assignment 'header_sec=malloc(reflen+20)', assigned value is 0
Rsubread/src/input-files.c:3166:20: note: Null pointer addition
Rsubread/src/input-files.c:4282:63: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/input-files.c:4273:23: note: Assuming allocation function fails
Rsubread/src/input-files.c:4273:23: note: Assignment 'names=malloc(orphant_fp_no*max_name_len)', assigned value is 0
Rsubread/src/input-files.c:4282:63: note: Null pointer addition
Rsubread/src/input-files.c:4505:21: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/input-files.c:4503:30: note: Assuming allocation function fails
Rsubread/src/input-files.c:4503:30: note: Assignment 'margin_data=malloc(save_start_pos+4)', assigned value is 0
Rsubread/src/input-files.c:4505:21: note: Null pointer addition
Rsubread/src/input-files.c:4608:12: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
Rsubread/src/input-files.c:4606:21: note: Assuming allocation function fails
Rsubread/src/input-files.c:4606:21: note: Assignment 'tb=malloc(Elen+Slen)', assigned value is 0
Rsubread/src/input-files.c:4608:12: note: Null pointer addition
Rsubread/src/input-files.c:5524:42: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary]
Rsubread/src/input-files.c:4694:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/input-files.c:4693:6: note: x1 is assigned
Rsubread/src/input-files.c:4694:6: note: x1 is overwritten
Rsubread/src/input-files.c:4695:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/input-files.c:4694:6: note: x1 is assigned
Rsubread/src/input-files.c:4695:6: note: x1 is overwritten
Rsubread/src/input-files.c:4696:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/input-files.c:4695:6: note: x1 is assigned
Rsubread/src/input-files.c:4696:6: note: x1 is overwritten
Rsubread/src/input-files.c:4698:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/input-files.c:4696:6: note: x1 is assigned
Rsubread/src/input-files.c:4698:6: note: x1 is overwritten
Rsubread/src/input-files.c:4700:6: style: Variable 'x1' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/input-files.c:4698:6: note: x1 is assigned
Rsubread/src/input-files.c:4700:6: note: x1 is overwritten
Rsubread/src/tx-unique.c:48:11: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_gene [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:47:20: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:47:20: note: Assignment 'tag_gene=malloc(sizeof(struct txunique_gene_t))', assigned value is 0
Rsubread/src/tx-unique.c:48:11: note: Null pointer dereference
Rsubread/src/tx-unique.c:49:3: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_gene [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:47:20: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:47:20: note: Assignment 'tag_gene=malloc(sizeof(struct txunique_gene_t))', assigned value is 0
Rsubread/src/tx-unique.c:49:3: note: Null pointer dereference
Rsubread/src/tx-unique.c:50:36: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_gene [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:47:20: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:47:20: note: Assignment 'tag_gene=malloc(sizeof(struct txunique_gene_t))', assigned value is 0
Rsubread/src/tx-unique.c:50:36: note: Null pointer dereference
Rsubread/src/tx-unique.c:51:39: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_gene [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:47:20: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:47:20: note: Assignment 'tag_gene=malloc(sizeof(struct txunique_gene_t))', assigned value is 0
Rsubread/src/tx-unique.c:51:39: note: Null pointer dereference
Rsubread/src/tx-unique.c:56:23: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_gene [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:47:20: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:47:20: note: Assignment 'tag_gene=malloc(sizeof(struct txunique_gene_t))', assigned value is 0
Rsubread/src/tx-unique.c:56:23: note: Null pointer dereference
Rsubread/src/tx-unique.c:66:11: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_tx [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:65:18: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:65:18: note: Assignment 'tag_tx=malloc(sizeof(struct txunique_transcript_t))', assigned value is 0
Rsubread/src/tx-unique.c:66:11: note: Null pointer dereference
Rsubread/src/tx-unique.c:67:3: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_tx [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:65:18: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:65:18: note: Assignment 'tag_tx=malloc(sizeof(struct txunique_transcript_t))', assigned value is 0
Rsubread/src/tx-unique.c:67:3: note: Null pointer dereference
Rsubread/src/tx-unique.c:68:36: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_tx [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:65:18: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:65:18: note: Assignment 'tag_tx=malloc(sizeof(struct txunique_transcript_t))', assigned value is 0
Rsubread/src/tx-unique.c:68:36: note: Null pointer dereference
Rsubread/src/tx-unique.c:73:10: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_exon [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:72:37: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:72:37: note: Assignment 'tag_exon=malloc(sizeof(struct txunique_exon_t))', assigned value is 0
Rsubread/src/tx-unique.c:73:10: note: Null pointer dereference
Rsubread/src/tx-unique.c:74:2: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_exon [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:72:37: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:72:37: note: Assignment 'tag_exon=malloc(sizeof(struct txunique_exon_t))', assigned value is 0
Rsubread/src/tx-unique.c:74:2: note: Null pointer dereference
Rsubread/src/tx-unique.c:75:2: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_exon [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:72:37: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:72:37: note: Assignment 'tag_exon=malloc(sizeof(struct txunique_exon_t))', assigned value is 0
Rsubread/src/tx-unique.c:75:2: note: Null pointer dereference
Rsubread/src/tx-unique.c:76:2: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_exon [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:72:37: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:72:37: note: Assignment 'tag_exon=malloc(sizeof(struct txunique_exon_t))', assigned value is 0
Rsubread/src/tx-unique.c:76:2: note: Null pointer dereference
Rsubread/src/tx-unique.c:77:16: warning: If memory allocation fails, then there is a possible null pointer dereference: tag_tx [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:65:18: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:65:18: note: Assignment 'tag_tx=malloc(sizeof(struct txunique_transcript_t))', assigned value is 0
Rsubread/src/tx-unique.c:77:16: note: Null pointer dereference
Rsubread/src/tx-unique.c:119:9: warning: If memory allocation fails, then there is a possible null pointer dereference: memex [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:118:34: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:118:34: note: Assignment 'memex=malloc(sizeof(struct txunique_exon_t))', assigned value is 0
Rsubread/src/tx-unique.c:119:9: note: Null pointer dereference
Rsubread/src/tx-unique.c:127:11: warning: If memory allocation fails, then there is a possible null pointer dereference: memex [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:126:36: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:126:36: note: Assignment 'memex=malloc(sizeof(struct txunique_exon_t))', assigned value is 0
Rsubread/src/tx-unique.c:127:11: note: Null pointer dereference
Rsubread/src/tx-unique.c:181:11: warning: If memory allocation fails, then there is a possible null pointer dereference: memex [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:180:36: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:180:36: note: Assignment 'memex=malloc(sizeof(struct txunique_exon_t))', assigned value is 0
Rsubread/src/tx-unique.c:181:11: note: Null pointer dereference
Rsubread/src/tx-unique.c:192:4: warning: If memory allocation fails, then there is a possible null pointer dereference: edge_start [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:191:52: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:191:52: note: Assignment 'edge_start=malloc(sizeof(struct _txunique_tmp_edges))', assigned value is 0
Rsubread/src/tx-unique.c:192:4: note: Null pointer dereference
Rsubread/src/tx-unique.c:193:4: warning: If memory allocation fails, then there is a possible null pointer dereference: edge_start [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:191:52: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:191:52: note: Assignment 'edge_start=malloc(sizeof(struct _txunique_tmp_edges))', assigned value is 0
Rsubread/src/tx-unique.c:193:4: note: Null pointer dereference
Rsubread/src/tx-unique.c:194:4: warning: If memory allocation fails, then there is a possible null pointer dereference: edge_start [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:191:52: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:191:52: note: Assignment 'edge_start=malloc(sizeof(struct _txunique_tmp_edges))', assigned value is 0
Rsubread/src/tx-unique.c:194:4: note: Null pointer dereference
Rsubread/src/tx-unique.c:195:4: warning: If memory allocation fails, then there is a possible null pointer dereference: edge_end [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:191:108: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:191:108: note: Assignment 'edge_end=malloc(sizeof(struct _txunique_tmp_edges))', assigned value is 0
Rsubread/src/tx-unique.c:195:4: note: Null pointer dereference
Rsubread/src/tx-unique.c:196:4: warning: If memory allocation fails, then there is a possible null pointer dereference: edge_end [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:191:108: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:191:108: note: Assignment 'edge_end=malloc(sizeof(struct _txunique_tmp_edges))', assigned value is 0
Rsubread/src/tx-unique.c:196:4: note: Null pointer dereference
Rsubread/src/tx-unique.c:197:4: warning: If memory allocation fails, then there is a possible null pointer dereference: edge_end [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:191:108: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:191:108: note: Assignment 'edge_end=malloc(sizeof(struct _txunique_tmp_edges))', assigned value is 0
Rsubread/src/tx-unique.c:197:4: note: Null pointer dereference
Rsubread/src/tx-unique.c:217:13: warning: If memory allocation fails, then there is a possible null pointer dereference: memedge [nullPointerOutOfMemory]
Rsubread/src/tx-unique.c:216:51: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:216:51: note: Assignment 'memedge=malloc(sizeof(struct _txunique_tmp_edges))', assigned value is 0
Rsubread/src/tx-unique.c:217:13: note: Null pointer dereference
Rsubread/src/tx-unique.c:366:10: warning: If resource allocation fails, then there is a possible null pointer dereference: out_fp [nullPointerOutOfResources]
Rsubread/src/tx-unique.c:365:23: note: Assuming allocation function fails
Rsubread/src/tx-unique.c:365:23: note: Assignment 'out_fp=fopen(context->output_file_name,"w")', assigned value is 0
Rsubread/src/tx-unique.c:366:10: note: Null pointer dereference
Rsubread/src/input-files.c:4001:50: warning: Either the condition 'all_threads<0' is redundant or there is division by zero at line 4001. [zerodivcond]
Rsubread/src/input-files.c:4001:18: note: Assuming that condition 'all_threads<0' is not redundant
Rsubread/src/input-files.c:4001:50: note: Division by zero
Rsubread/src/tx-unique.c:126:22: style: Local variable 'memex' shadows outer variable [shadowVariable]
Rsubread/src/tx-unique.c:118:20: note: Shadowed declaration
Rsubread/src/tx-unique.c:126:22: note: Shadow variable
Rsubread/src/input-files.c:104:67: style:inconclusive: Function 'guess_reads_density_format' argument 3 names different: declaration 'min_phred' definition 'min_phred_score'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:283:67: note: Function 'guess_reads_density_format' argument 3 names different: declaration 'min_phred' definition 'min_phred_score'.
Rsubread/src/input-files.c:104:67: note: Function 'guess_reads_density_format' argument 3 names different: declaration 'min_phred' definition 'min_phred_score'.
Rsubread/src/input-files.c:104:90: style:inconclusive: Function 'guess_reads_density_format' argument 4 names different: declaration 'max_phred' definition 'max_phred_score'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:283:84: note: Function 'guess_reads_density_format' argument 4 names different: declaration 'max_phred' definition 'max_phred_score'.
Rsubread/src/input-files.c:104:90: note: Function 'guess_reads_density_format' argument 4 names different: declaration 'max_phred' definition 'max_phred_score'.
Rsubread/src/input-files.c:265:19: style:inconclusive: Function 'read_line' argument 1 names different: declaration 'max_len' definition 'max_read_len'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:249:19: note: Function 'read_line' argument 1 names different: declaration 'max_len' definition 'max_read_len'.
Rsubread/src/input-files.c:265:19: note: Function 'read_line' argument 1 names different: declaration 'max_len' definition 'max_read_len'.
Rsubread/src/input-files.c:265:61: style:inconclusive: Function 'read_line' argument 4 names different: declaration 'conv_to_upper' definition 'must_upper'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:249:56: note: Function 'read_line' argument 4 names different: declaration 'conv_to_upper' definition 'must_upper'.
Rsubread/src/input-files.c:265:61: note: Function 'read_line' argument 4 names different: declaration 'conv_to_upper' definition 'must_upper'.
Rsubread/src/input-files.c:346:51: style:inconclusive: Function 'geinput_readline' argument 2 names different: declaration 'linebuffer' definition 'buff'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:242:51: note: Function 'geinput_readline' argument 2 names different: declaration 'linebuffer' definition 'buff'.
Rsubread/src/input-files.c:346:51: note: Function 'geinput_readline' argument 2 names different: declaration 'linebuffer' definition 'buff'.
Rsubread/src/input-files.c:390:35: style:inconclusive: Function 'geinput_open_scRNA_BAM' argument 1 names different: declaration 'fnames' definition 'rfnames'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:344:35: note: Function 'geinput_open_scRNA_BAM' argument 1 names different: declaration 'fnames' definition 'rfnames'.
Rsubread/src/input-files.c:390:35: note: Function 'geinput_open_scRNA_BAM' argument 1 names different: declaration 'fnames' definition 'rfnames'.
Rsubread/src/input-files.c:398:35: style:inconclusive: Function 'geinput_open_scRNA_fqs' argument 1 names different: declaration 'fnames' definition 'rfnames'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:343:35: note: Function 'geinput_open_scRNA_fqs' argument 1 names different: declaration 'fnames' definition 'rfnames'.
Rsubread/src/input-files.c:398:35: note: Function 'geinput_open_scRNA_fqs' argument 1 names different: declaration 'fnames' definition 'rfnames'.
Rsubread/src/input-files.c:406:73: style:inconclusive: Function 'geinput_open_bcl' argument 3 names different: declaration 'reads_in_chunk' definition 'reads_per_chunk'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:345:73: note: Function 'geinput_open_bcl' argument 3 names different: declaration 'reads_in_chunk' definition 'reads_per_chunk'.
Rsubread/src/input-files.c:406:73: note: Function 'geinput_open_bcl' argument 3 names different: declaration 'reads_in_chunk' definition 'reads_per_chunk'.
Rsubread/src/input-files.c:415:71: style:inconclusive: Function 'geinput_open_sam' argument 3 names different: declaration 'half_no' definition 'half_number'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:217:71: note: Function 'geinput_open_sam' argument 3 names different: declaration 'half_no' definition 'half_number'.
Rsubread/src/input-files.c:415:71: note: Function 'geinput_open_sam' argument 3 names different: declaration 'half_no' definition 'half_number'.
Rsubread/src/input-files.c:641:56: style:inconclusive: Function 'geinput_readline_back' argument 2 names different: declaration 'linebuffer' definition 'linebuffer_3000'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:220:56: note: Function 'geinput_readline_back' argument 2 names different: declaration 'linebuffer' definition 'linebuffer_3000'.
Rsubread/src/input-files.c:641:56: note: Function 'geinput_readline_back' argument 2 names different: declaration 'linebuffer' definition 'linebuffer_3000'.
Rsubread/src/input-files.c:1113:26: style:inconclusive: Function 'reverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:259:26: note: Function 'reverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'.
Rsubread/src/input-files.c:1113:26: note: Function 'reverse_read' argument 1 names different: declaration 'ReadString' definition 'InBuff'.
Rsubread/src/input-files.c:1113:38: style:inconclusive: Function 'reverse_read' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:259:42: note: Function 'reverse_read' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/input-files.c:1113:38: note: Function 'reverse_read' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/input-files.c:1192:29: style:inconclusive: Function 'reverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:261:29: note: Function 'reverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'.
Rsubread/src/input-files.c:1192:29: note: Function 'reverse_quality' argument 1 names different: declaration 'QualtyString' definition 'InBuff'.
Rsubread/src/input-files.c:1192:41: style:inconclusive: Function 'reverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:261:47: note: Function 'reverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/input-files.c:1192:41: note: Function 'reverse_quality' argument 2 names different: declaration 'Length' definition 'read_len'.
Rsubread/src/input-files.c:1576:312: style:inconclusive: Function 'write_read_block_file' argument 16 names different: declaration 'M_seg' definition 'mapped_seg'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:287:312: note: Function 'write_read_block_file' argument 16 names different: declaration 'M_seg' definition 'mapped_seg'.
Rsubread/src/input-files.c:1576:312: note: Function 'write_read_block_file' argument 16 names different: declaration 'M_seg' definition 'mapped_seg'.
Rsubread/src/input-files.c:1854:44: style:inconclusive: Function 'break_SAM_file' argument 2 names different: declaration 'is_BAM' definition 'is_BAM_file'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:272:44: note: Function 'break_SAM_file' argument 2 names different: declaration 'is_BAM' definition 'is_BAM_file'.
Rsubread/src/input-files.c:1854:44: note: Function 'break_SAM_file' argument 2 names different: declaration 'is_BAM' definition 'is_BAM_file'.
Rsubread/src/input-files.c:1854:120: style:inconclusive: Function 'break_SAM_file' argument 5 names different: declaration 'block_no' definition 'block_count'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:272:115: note: Function 'break_SAM_file' argument 5 names different: declaration 'block_no' definition 'block_count'.
Rsubread/src/input-files.c:1854:120: note: Function 'break_SAM_file' argument 5 names different: declaration 'block_no' definition 'block_count'.
Rsubread/src/input-files.c:1854:288: style:inconclusive: Function 'break_SAM_file' argument 11 names different: declaration 'all_Mapped_bases' definition 'all_mapped_bases'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:272:280: note: Function 'break_SAM_file' argument 11 names different: declaration 'all_Mapped_bases' definition 'all_mapped_bases'.
Rsubread/src/input-files.c:1854:288: note: Function 'break_SAM_file' argument 11 names different: declaration 'all_Mapped_bases' definition 'all_mapped_bases'.
Rsubread/src/input-files.c:1854:318: style:inconclusive: Function 'break_SAM_file' argument 12 names different: declaration 'event_table_ptr' definition 'event_table'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:272:311: note: Function 'break_SAM_file' argument 12 names different: declaration 'event_table_ptr' definition 'event_table'.
Rsubread/src/input-files.c:1854:318: note: Function 'break_SAM_file' argument 12 names different: declaration 'event_table_ptr' definition 'event_table'.
Rsubread/src/input-files.c:1854:431: style:inconclusive: Function 'break_SAM_file' argument 17 names different: declaration 'use_soft_clipped_bases' definition 'use_softclipped_bases'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:272:428: note: Function 'break_SAM_file' argument 17 names different: declaration 'use_soft_clipped_bases' definition 'use_softclipped_bases'.
Rsubread/src/input-files.c:1854:431: note: Function 'break_SAM_file' argument 17 names different: declaration 'use_soft_clipped_bases' definition 'use_softclipped_bases'.
Rsubread/src/input-files.c:2280:28: style:inconclusive: Function 'does_file_exist' argument 1 names different: declaration 'filename' definition 'path'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:281:29: note: Function 'does_file_exist' argument 1 names different: declaration 'filename' definition 'path'.
Rsubread/src/input-files.c:2280:28: note: Function 'does_file_exist' argument 1 names different: declaration 'filename' definition 'path'.
Rsubread/src/input-files.c:2384:106: style:inconclusive: Function 'SAM_pairer_writer_create' argument 4 names different: declaration 'BAM_output' definition 'BAM_input'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:328:106: note: Function 'SAM_pairer_writer_create' argument 4 names different: declaration 'BAM_output' definition 'BAM_input'.
Rsubread/src/input-files.c:2384:106: note: Function 'SAM_pairer_writer_create' argument 4 names different: declaration 'BAM_output' definition 'BAM_input'.
Rsubread/src/input-files.c:2384:121: style:inconclusive: Function 'SAM_pairer_writer_create' argument 5 names different: declaration 'BAM_compression_level' definition 'c_level'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:328:122: note: Function 'SAM_pairer_writer_create' argument 5 names different: declaration 'BAM_compression_level' definition 'c_level'.
Rsubread/src/input-files.c:2384:121: note: Function 'SAM_pairer_writer_create' argument 5 names different: declaration 'BAM_compression_level' definition 'c_level'.
Rsubread/src/input-files.c:3427:40: style:inconclusive: Function 'SAP_pairer_skip_tag_body_len' argument 1 names different: declaration 'tag_start' definition 'bin'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:327:41: note: Function 'SAP_pairer_skip_tag_body_len' argument 1 names different: declaration 'tag_start' definition 'bin'.
Rsubread/src/input-files.c:3427:40: note: Function 'SAP_pairer_skip_tag_body_len' argument 1 names different: declaration 'tag_start' definition 'bin'.
Rsubread/src/input-files.c:3600:41: style:inconclusive: Function 'SAM_pairer_get_tag_bin_start' argument 1 names different: declaration 'bin' definition 'bin1'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:333:41: note: Function 'SAM_pairer_get_tag_bin_start' argument 1 names different: declaration 'bin' definition 'bin1'.
Rsubread/src/input-files.c:3600:41: note: Function 'SAM_pairer_get_tag_bin_start' argument 1 names different: declaration 'bin' definition 'bin1'.
Rsubread/src/input-files.c:3776:38: style:inconclusive: Function 'SAM_pairer_writer_reset' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:322:37: note: Function 'SAM_pairer_writer_reset' argument 1 names different: declaration 'pairer' definition 'pairer_vp'.
Rsubread/src/input-files.c:3776:38: note: Function 'SAM_pairer_writer_reset' argument 1 names different: declaration 'pairer' definition 'pairer_vp'.
Rsubread/src/input-files.c:3793:43: style:inconclusive: Function 'SAM_pairer_multi_thread_output' argument 1 names different: declaration 'pairer' definition 'pairer_vp'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:325:44: note: Function 'SAM_pairer_multi_thread_output' argument 1 names different: declaration 'pairer' definition 'pairer_vp'.
Rsubread/src/input-files.c:3793:43: note: Function 'SAM_pairer_multi_thread_output' argument 1 names different: declaration 'pairer' definition 'pairer_vp'.
Rsubread/src/input-files.c:4474:61: style:inconclusive: Function 'is_read_bin' argument 4 names different: declaration 'tiny_mod' definition 'tiny_mode'. [funcArgNamesDifferent]
Rsubread/src/input-files.c:2944:61: note: Function 'is_read_bin' argument 4 names different: declaration 'tiny_mod' definition 'tiny_mode'.
Rsubread/src/input-files.c:4474:61: note: Function 'is_read_bin' argument 4 names different: declaration 'tiny_mod' definition 'tiny_mode'.
Rsubread/src/input-files.c:6258:47: style:inconclusive: Function 'is_certainly_bam_file' argument 2 names different: declaration 'is_firstread_PE' definition 'is_first_read_PE'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:304:47: note: Function 'is_certainly_bam_file' argument 2 names different: declaration 'is_firstread_PE' definition 'is_first_read_PE'.
Rsubread/src/input-files.c:6258:47: note: Function 'is_certainly_bam_file' argument 2 names different: declaration 'is_firstread_PE' definition 'is_first_read_PE'.
Rsubread/src/input-files.c:6258:76: style:inconclusive: Function 'is_certainly_bam_file' argument 3 names different: declaration 'SAMBAM_header_length' definition 'SAMBAM_header_size'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:304:76: note: Function 'is_certainly_bam_file' argument 3 names different: declaration 'SAMBAM_header_length' definition 'SAMBAM_header_size'.
Rsubread/src/input-files.c:6258:76: note: Function 'is_certainly_bam_file' argument 3 names different: declaration 'SAMBAM_header_length' definition 'SAMBAM_header_size'.
Rsubread/src/input-files.c:6486:41: style:inconclusive: Function 'probe_file_type' argument 2 names different: declaration 'is_first_PE' definition 'is_first_read_PE'. [funcArgNamesDifferent]
Rsubread/src/input-files.h:311:41: note: Function 'probe_file_type' argument 2 names different: declaration 'is_first_PE' definition 'is_first_read_PE'.
Rsubread/src/input-files.c:6486:41: note: Function 'probe_file_type' argument 2 names different: declaration 'is_first_PE' definition 'is_first_read_PE'.
Rsubread/src/tx-unique.c:40:33: style: Parameter 'gene_name' can be declared as pointer to const. However it seems that 'txunique_do_add_exon' is a callback function, if 'gene_name' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/tx-unique.c:83:207: note: You might need to cast the function pointer here
Rsubread/src/tx-unique.c:40:33: note: Parameter 'gene_name' can be declared as pointer to const
Rsubread/src/tx-unique.c:40:51: style: Parameter 'transcript_id' can be declared as pointer to const. However it seems that 'txunique_do_add_exon' is a callback function, if 'transcript_id' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/tx-unique.c:83:207: note: You might need to cast the function pointer here
Rsubread/src/tx-unique.c:40:51: note: Parameter 'transcript_id' can be declared as pointer to const
Rsubread/src/tx-unique.c:40:73: style: Parameter 'chrome_name' can be declared as pointer to const. However it seems that 'txunique_do_add_exon' is a callback function, if 'chrome_name' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/tx-unique.c:83:207: note: You might need to cast the function pointer here
Rsubread/src/tx-unique.c:40:73: note: Parameter 'chrome_name' can be declared as pointer to const
Rsubread/src/tx-unique.c:88:70: style: Parameter 'me' can be declared as pointer to const. However it seems that 'txunique_process_flat_comp' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/tx-unique.c:113:22: note: You might need to cast the function pointer here
Rsubread/src/tx-unique.c:88:70: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/tx-unique.c:89:20: style: Variable 'ex1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:90:20: style: Variable 'ex2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:153:72: style: Parameter 'me' can be declared as pointer to const. However it seems that 'txunique_process_gene_edge_comp' is a callback function, if 'me' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
Rsubread/src/tx-unique.c:205:29: note: You might need to cast the function pointer here
Rsubread/src/tx-unique.c:153:72: note: Parameter 'me' can be declared as pointer to const
Rsubread/src/tx-unique.c:154:31: style: Variable 'e1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:155:31: style: Variable 'e2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:164:70: style: Parameter 'chro' can be declared as pointer to const [constParameterPointer]
Rsubread/src/tx-unique.c:178:22: style: Variable 'try_ex' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:190:22: style: Variable 'try_ex' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:234:24: style: Variable 'txex' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:236:34: style: Variable 'edge' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:311:23: style: Variable 'context' can be declared as pointer to const [constVariablePointer]
Rsubread/src/tx-unique.c:340:12: style: Variable 't_chro' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:4201:10: style: Local variable 'tmp_fname' shadows outer variable [shadowVariable]
Rsubread/src/input-files.c:4143:7: note: Shadowed declaration
Rsubread/src/input-files.c:4201:10: note: Shadow variable
Rsubread/src/input-files.c:5263:7: style: Local variable 'x1' shadows outer variable [shadowVariable]
Rsubread/src/input-files.c:5240:6: note: Shadowed declaration
Rsubread/src/input-files.c:5263:7: note: Shadow variable
Rsubread/src/input-files.c:81:25: style: Parameter 'in' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:97:35: style: Variable 'ct' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:104:42: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:351:20: style: Parameter 'in_buff' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:601:12: style: Variable 'fgin' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:1207:25: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1232:23: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1253:40: style: Parameter 'key' can be declared as const array [constParameter]
Rsubread/src/input-files.c:1418:27: style: Parameter 'sam_line' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1531:36: style: Parameter 'temp_file_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1576:168: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1576:185: style: Parameter 'quality_string' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1621:10: style: Variable 'is_ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:1672:64: style: Parameter 'chro' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1672:113: style: Parameter 'ins_seq' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1776:28: style: Parameter 'vcf_file' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1803:10: style: Variable 'pos_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:1809:10: style: Variable 'ref_seq' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:1818:11: style: Variable 'com_sec' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:1854:268: style: Parameter 'offsets' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:1900:10: style: Variable 'is_ret' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:2162:36: style: Parameter 'output_genes' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2185:94: style: Parameter 'offsets' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2280:28: style: Parameter 'path' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2290:32: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2373:30: style: Parameter 'prefix' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2384:137: style: Parameter 'out_file' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2544:32: style: Parameter 'in_file' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2562:511: style: Parameter 'tmp_path' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:2662:47: style: Parameter 'hashed_obj' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:3094:13: style: Variable 'sqname' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:3188:92: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:3451:70: style: Parameter 'tag_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:3570:110: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:3600:41: style: Parameter 'bin1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:3610:9: style: Variable 'realname' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:3793:89: style: Parameter 'bin2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:3829:128: style: Parameter 'read_full_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:3979:41: style: Parameter 'st' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:4029:41: style: Parameter 'c1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:4029:52: style: Parameter 'c2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:4047:59: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:4129:56: style: Parameter 'pairer' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:4577:59: style: Parameter 'pairer' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:4590:9: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:4595:10: style: Variable 'Sbin' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:4596:10: style: Variable 'Ebin' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:5253:8: style: Variable 'NOSORT_SAM_eof' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:5347:10: style: Variable 'header_start' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:5380:12: style: Variable 'sqname' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:5648:54: style: Parameter 'output_file' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:5691:9: style: Variable 'hi_tag_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:5854:13: style: Variable 'first_read_text' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:5874:14: style: Variable 'dummy_mate_chr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:5961:14: style: Variable 'dummy_mate_chr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6064:10: style: Variable 'second_col_pos' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6116:10: style: Variable 'hi_tag_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6211:28: style: Parameter 'SAM_line' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:6270:25: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:6383:33: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:6399:11: style: Variable 'rptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6462:11: style: Variable 'rptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6508:11: style: Variable 'rptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6545:11: style: Variable 'rptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6604:11: style: Variable 'rptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6631:12: style: Variable 'tbr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6649:60: style: Parameter 't2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:6652:10: style: Variable 't1chro' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6654:10: style: Variable 't2chro' can be declared as pointer to const [constVariablePointer]
Rsubread/src/input-files.c:6664:52: style: Parameter 't2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/input-files.c:315:12: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
Rsubread/src/input-files.c:333:12: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
Rsubread/src/input-files.c:666:5: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
Rsubread/src/input-files.c:673:3: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
Rsubread/src/input-files.c:674:6: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack]
Rsubread/src/input-files.c:1708:38: portability: 'event_table_ptr->appendix2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/input-files.c:4597:20: portability: 'tab->appendix2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/input-files.c:4616:25: portability: 'tab->appendix2' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/input-files.c:2979:81: warning: Either the condition 'header_txt_dynamic_length>0' is redundant or there is signed integer overflow for expression 'header_txt_dynamic_length-1000000'. [integerOverflowCond]
Rsubread/src/input-files.c:2979:35: note: Assuming that condition 'header_txt_dynamic_length>0' is not redundant
Rsubread/src/input-files.c:2979:81: note: Integer overflow
Rsubread/src/input-files.c:2953:5: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
Rsubread/src/input-files.c:2953:5: note: Assignment 'nch=-1', assigned value is -1
Rsubread/src/input-files.c:2953:5: note: Negative value is converted to an unsigned value
Rsubread/src/input-files.c:2954:5: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
Rsubread/src/input-files.c:2954:5: note: Assignment 'nch=-1', assigned value is -1
Rsubread/src/input-files.c:2954:5: note: Negative value is converted to an unsigned value
Rsubread/src/input-files.c:2967:5: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
Rsubread/src/input-files.c:2967:5: note: Assignment 'nch=-1', assigned value is -1
Rsubread/src/input-files.c:2967:5: note: Negative value is converted to an unsigned value
Rsubread/src/input-files.c:2971:6: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
Rsubread/src/input-files.c:2971:6: note: Assignment 'nch=-1', assigned value is -1
Rsubread/src/input-files.c:2971:6: note: Negative value is converted to an unsigned value
Rsubread/src/input-files.c:2990:6: warning: Expression 'nch' can have a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
Rsubread/src/input-files.c:2990:6: note: Assignment 'nch=-1', assigned value is -1
Rsubread/src/input-files.c:2990:6: note: Negative value is converted to an unsigned value
Rsubread/src/input-files.c:107:16: style: Variable 'fpos' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:107:26: style: Variable 'fpos2' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:520:11: style: Variable 'rlen' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:529:11: style: Variable 'rlen' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:901:10: style: Variable 'tr' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:1679:30: style: Variable 'indel_event_id' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:2670:24: style: Variable 'all_orphants' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:2679:16: style: Variable 'all_orphants' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:2948:11: style: Variable 'nch' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:2953:5: style: Variable 'bam_signature' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:3244:14: style: Variable 'seq_len' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:3244:6: style: Variable 'seq_len' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:4700:6: style: Variable 'x1' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:4867:14: style: Variable 'nch' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:4924:14: style: Variable 'seq_len' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:4924:28: style: Variable 'name_len' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:4924:44: style: Variable 'cigar_opts' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5074:14: style: Variable 'seq_len' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5075:30: style: Variable 'sqlen_ptr' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5077:17: style: Variable 'cigar_opts' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5265:3: style: Variable 'bam_signature' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5498:46: style: Variable 'block_size' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5522:15: style: Variable 'nch' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5524:16: style: Variable 'disk_is_full' is assigned a value that is never used. [unreadVariable]
Rsubread/src/input-files.c:5501:15: style: Variable 'bam_buffer' is allocated memory that is never used. [unusedAllocatedMemory]
Rsubread/src/readSummary.c:2610:4: warning: Return value of function deflateInit2() is not used. [ignoredReturnValue]
Rsubread/src/readSummary.c:2615:4: warning: Return value of function deflate() is not used. [ignoredReturnValue]
Rsubread/src/readSummary.c:1974:8: style: Condition '0&&FIXLENstrcmp("V0112_0155:7:1101:20072:12961#ATCAC",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/readSummary.c:2001:7: style: Condition '0&&FIXLENstrcmp("V0112_0155:7:1101:20072:12961#ATCAC",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/readSummary.c:3006:8: style: Condition '1||global_context->is_paired_end_mode_assign' is always true [knownConditionTrueFalse]
Rsubread/src/readSummary.c:3269:17: style: Condition '0&&FIXLENstrcmp("V0112_0155:7:1101:10214:3701",read_name)==0' is always false [knownConditionTrueFalse]
Rsubread/src/readSummary.c:3293:6: style: Condition '0&&global_context->do_junction_counting' is always false [knownConditionTrueFalse]
Rsubread/src/readSummary.c:4492:7: style: Condition '0&&assign_ret' is always false [knownConditionTrueFalse]
Rsubread/src/readSummary.c:5242:29: style: Condition 'c1==c2' is always true [knownConditionTrueFalse]
Rsubread/src/readSummary.c:5242:15: note: Assuming that condition 'c1=='\t'' is not redundant
Rsubread/src/readSummary.c:5242:29: note: Condition 'c1==c2' is always true
Rsubread/src/readSummary.c:5251:20: style: Condition 'c2==0' is always false [knownConditionTrueFalse]
Rsubread/src/readSummary.c:4864:3: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
Rsubread/src/readSummary.c:938:16: error: Memory leak: file_line [memleak]
Rsubread/src/readSummary.c:2506:3: error: Memory leak: ret [memleak]
Rsubread/src/readSummary.c:6330:19: error: Memory leak: line [memleak]
Rsubread/src/readSummary.c:6335:3: error: Memory leak: line [memleak]
Rsubread/src/readSummary.c:1042:5: error: Common realloc mistake: 'ret_features' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1160:6: error: Common realloc mistake: 'ret_features' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1225:9: error: Common realloc mistake: 'extcols' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1590:6: error: Common realloc mistake: 'ret_block_min_start' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1591:6: error: Common realloc mistake: 'ret_block_max_end' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1592:6: error: Common realloc mistake: 'ret_block_end_index' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1617:5: error: Common realloc mistake: 'ret_block_min_start' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1618:5: error: Common realloc mistake: 'ret_block_max_end' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:1619:5: error: Common realloc mistake: 'ret_block_end_index' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:6446:4: error: Common realloc mistake: 'cmd_rebuilt' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:6765:4: error: Common realloc mistake: 'very_long_file_names' nulled but not freed upon failure [memleakOnRealloc]
Rsubread/src/readSummary.c:608:20: warning: If memory allocation fails, then there is a possible null pointer dereference: sam_used [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:602:56: note: Assuming allocation function fails
Rsubread/src/readSummary.c:602:56: note: Assignment 'sam_used=malloc(strlen(sam)+1000)', assigned value is 0
Rsubread/src/readSummary.c:608:20: note: Null pointer dereference
Rsubread/src/readSummary.c:617:9: warning: If memory allocation fails, then there is a possible null pointer dereference: sam_used [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:602:56: note: Assuming allocation function fails
Rsubread/src/readSummary.c:602:56: note: Assignment 'sam_used=malloc(strlen(sam)+1000)', assigned value is 0
Rsubread/src/readSummary.c:617:9: note: Null pointer dereference
Rsubread/src/readSummary.c:698:2: warning: If memory allocation fails, then there is a possible null pointer dereference: PEexpectStr [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:681:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:681:29: note: Assignment 'PEexpectStr=malloc(nfiles*6)', assigned value is 0
Rsubread/src/readSummary.c:698:2: note: Null pointer dereference
Rsubread/src/readSummary.c:698:21: warning: If memory allocation fails, then there is a possible null pointer dereference: PEexpectStr [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:681:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:681:29: note: Assignment 'PEexpectStr=malloc(nfiles*6)', assigned value is 0
Rsubread/src/readSummary.c:698:21: note: Null pointer dereference
Rsubread/src/readSummary.c:711:2: warning: If memory allocation fails, then there is a possible null pointer dereference: PEassignStr [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:680:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:680:29: note: Assignment 'PEassignStr=malloc(nfiles*6)', assigned value is 0
Rsubread/src/readSummary.c:711:2: note: Null pointer dereference
Rsubread/src/readSummary.c:711:21: warning: If memory allocation fails, then there is a possible null pointer dereference: PEassignStr [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:680:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:680:29: note: Assignment 'PEassignStr=malloc(nfiles*6)', assigned value is 0
Rsubread/src/readSummary.c:711:21: note: Null pointer dereference
Rsubread/src/readSummary.c:845:10: warning: If memory allocation fails, then there is a possible null pointer dereference: new_name [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:844:27: note: Assuming allocation function fails
Rsubread/src/readSummary.c:844:27: note: Assignment 'new_name=malloc(strlen(chro)+1)', assigned value is 0
Rsubread/src/readSummary.c:845:10: note: Null pointer dereference
Rsubread/src/readSummary.c:851:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_info [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:850:21: note: Assuming allocation function fails
Rsubread/src/readSummary.c:850:21: note: Assignment 'gene_info=malloc(sizeof(struct fc_junction_gene_t))', assigned value is 0
Rsubread/src/readSummary.c:851:3: note: Null pointer dereference
Rsubread/src/readSummary.c:852:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_info [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:850:21: note: Assuming allocation function fails
Rsubread/src/readSummary.c:850:21: note: Assignment 'gene_info=malloc(sizeof(struct fc_junction_gene_t))', assigned value is 0
Rsubread/src/readSummary.c:852:3: note: Null pointer dereference
Rsubread/src/readSummary.c:853:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_info [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:850:21: note: Assuming allocation function fails
Rsubread/src/readSummary.c:850:21: note: Assignment 'gene_info=malloc(sizeof(struct fc_junction_gene_t))', assigned value is 0
Rsubread/src/readSummary.c:853:3: note: Null pointer dereference
Rsubread/src/readSummary.c:855:28: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_info [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:850:21: note: Assuming allocation function fails
Rsubread/src/readSummary.c:850:21: note: Assignment 'gene_info=malloc(sizeof(struct fc_junction_gene_t))', assigned value is 0
Rsubread/src/readSummary.c:855:28: note: Null pointer dereference
Rsubread/src/readSummary.c:1069:25: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/readSummary.c:1066:36: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/readSummary.c:1064:29: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1063:11: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1069:25: note: Null pointer dereference
Rsubread/src/readSummary.c:1070:25: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck]
Rsubread/src/readSummary.c:1066:36: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/readSummary.c:1064:29: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1064:19: note: end_ptr is assigned 'strtok_r(NULL,"\t",&token_temp)' here.
Rsubread/src/readSummary.c:1070:25: note: Null pointer dereference
Rsubread/src/readSummary.c:1072:16: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/readSummary.c:1066:36: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/readSummary.c:1064:29: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1063:11: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1072:16: note: Null pointer dereference
Rsubread/src/readSummary.c:1095:34: warning: Either the condition 'strand_str==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck]
Rsubread/src/readSummary.c:1103:18: note: Assuming that condition 'strand_str==NULL' is not redundant
Rsubread/src/readSummary.c:1102:32: note: Assignment to 'strand_str=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1064:19: note: end_ptr is assigned 'strtok_r(NULL,"\t",&token_temp)' here.
Rsubread/src/readSummary.c:1095:34: note: Null pointer dereference
Rsubread/src/readSummary.c:1127:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1127:5: note: Null pointer dereference
Rsubread/src/readSummary.c:1128:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1128:5: note: Null pointer dereference
Rsubread/src/readSummary.c:1129:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1129:5: note: Null pointer dereference
Rsubread/src/readSummary.c:1130:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1130:5: note: Null pointer dereference
Rsubread/src/readSummary.c:1130:54: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1130:54: note: Null pointer dereference
Rsubread/src/readSummary.c:1133:4: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1133:4: note: Null pointer dereference
Rsubread/src/readSummary.c:1135:8: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1135:8: note: Null pointer dereference
Rsubread/src/readSummary.c:1135:45: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1135:45: note: Null pointer dereference
Rsubread/src/readSummary.c:1169:26: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/readSummary.c:1166:37: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/readSummary.c:1164:30: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1163:12: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1169:26: note: Null pointer dereference
Rsubread/src/readSummary.c:1170:26: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: end_ptr. [nullPointerRedundantCheck]
Rsubread/src/readSummary.c:1166:37: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/readSummary.c:1164:30: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1164:20: note: end_ptr is assigned 'strtok_r(NULL,"\t",&token_temp)' here.
Rsubread/src/readSummary.c:1170:26: note: Null pointer dereference
Rsubread/src/readSummary.c:1172:17: warning: Either the condition 'end_ptr==NULL' is redundant or there is possible null pointer dereference: start_ptr. [nullPointerRedundantCheck]
Rsubread/src/readSummary.c:1166:37: note: Assuming that condition 'end_ptr==NULL' is not redundant
Rsubread/src/readSummary.c:1164:30: note: Assignment to 'end_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1163:12: note: Assignment from 'start_ptr=strtok_r(NULL,"\t",&token_temp)'
Rsubread/src/readSummary.c:1172:17: note: Null pointer dereference
Rsubread/src/readSummary.c:1273:6: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1273:6: note: Null pointer dereference
Rsubread/src/readSummary.c:1274:6: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1274:6: note: Null pointer dereference
Rsubread/src/readSummary.c:1275:6: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1275:6: note: Null pointer dereference
Rsubread/src/readSummary.c:1276:6: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1276:6: note: Null pointer dereference
Rsubread/src/readSummary.c:1276:55: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1276:55: note: Null pointer dereference
Rsubread/src/readSummary.c:1279:5: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1279:5: note: Null pointer dereference
Rsubread/src/readSummary.c:1281:9: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1281:9: note: Null pointer dereference
Rsubread/src/readSummary.c:1281:46: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
Rsubread/src/readSummary.c:1281:46: note: Null pointer dereference
Rsubread/src/readSummary.c:1402:27: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_start [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1370:31: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1370:31: note: Assignment 'tmp_start=malloc(sizeof(long long)*total_items)', assigned value is 0
Rsubread/src/readSummary.c:1402:27: note: Null pointer dereference
Rsubread/src/readSummary.c:1403:25: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_end [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1371:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1371:29: note: Assignment 'tmp_end=malloc(sizeof(long long)*total_items)', assigned value is 0
Rsubread/src/readSummary.c:1403:25: note: Null pointer dereference
Rsubread/src/readSummary.c:1404:28: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_strand [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1372:37: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1372:37: note: Assignment 'tmp_strand=malloc(sizeof(char)*total_items)', assigned value is 0
Rsubread/src/readSummary.c:1404:28: note: Null pointer dereference
Rsubread/src/readSummary.c:1405:29: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_entyrez [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1373:28: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1373:28: note: Assignment 'tmp_entyrez=malloc(sizeof(int)*total_items)', assigned value is 0
Rsubread/src/readSummary.c:1405:29: note: Null pointer dereference
Rsubread/src/readSummary.c:1406:30: warning: If memory allocation fails, then there is a possible null pointer dereference: tmp_info_ptr [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1374:44: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1374:44: note: Assignment 'tmp_info_ptr=malloc(sizeof(struct fc_feature_info_t*)*total_items)', assigned value is 0
Rsubread/src/readSummary.c:1406:30: note: Null pointer dereference
Rsubread/src/readSummary.c:1555:4: warning: If memory allocation fails, then there is a possible null pointer dereference: features_per_block_bins [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1552:43: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1552:43: note: Assignment 'features_per_block_bins=malloc(sizeof(short)*bins_in_chr)', assigned value is 0
Rsubread/src/readSummary.c:1555:4: note: Null pointer dereference
Rsubread/src/readSummary.c:1709:2: warning: If memory allocation fails, then there is a possible null pointer dereference: out_buf1 [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1691:25: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1691:25: note: Assignment 'out_buf1=malloc(read_length+spaces*refill_spaces+1)', assigned value is 0
Rsubread/src/readSummary.c:1709:2: note: Null pointer dereference
Rsubread/src/readSummary.c:1716:15: warning: If memory allocation fails, then there is a possible null pointer dereference: out_buf1 [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:1691:25: note: Assuming allocation function fails
Rsubread/src/readSummary.c:1691:25: note: Assignment 'out_buf1=malloc(read_length+spaces*refill_spaces+1)', assigned value is 0
Rsubread/src/readSummary.c:1716:15: note: Null pointer dereference
Rsubread/src/readSummary.c:2482:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:2480:14: note: Assuming allocation function fails
Rsubread/src/readSummary.c:2480:14: note: Assignment 'ret=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/readSummary.c:2482:2: note: Null pointer dereference
Rsubread/src/readSummary.c:2483:2: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:2480:14: note: Assuming allocation function fails
Rsubread/src/readSummary.c:2480:14: note: Assignment 'ret=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/readSummary.c:2483:2: note: Null pointer dereference
Rsubread/src/readSummary.c:2485:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:2480:14: note: Assuming allocation function fails
Rsubread/src/readSummary.c:2480:14: note: Assignment 'ret=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/readSummary.c:2485:9: note: Null pointer dereference
Rsubread/src/readSummary.c:2486:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:2480:14: note: Assuming allocation function fails
Rsubread/src/readSummary.c:2480:14: note: Assignment 'ret=malloc(sizeof(void*)*4)', assigned value is 0
Rsubread/src/readSummary.c:2486:9: note: Null pointer dereference
Rsubread/src/readSummary.c:3908:7: warning: If memory allocation fails, then there is a possible null pointer dereference: rg_old_tabs [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:3907:27: note: Assuming allocation function fails
Rsubread/src/readSummary.c:3907:27: note: Assignment 'rg_old_tabs=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/readSummary.c:3908:7: note: Null pointer dereference
Rsubread/src/readSummary.c:3909:7: warning: If memory allocation fails, then there is a possible null pointer dereference: rg_old_tabs [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:3907:27: note: Assuming allocation function fails
Rsubread/src/readSummary.c:3907:27: note: Assignment 'rg_old_tabs=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/readSummary.c:3909:7: note: Null pointer dereference
Rsubread/src/readSummary.c:3927:29: warning: If memory allocation fails, then there is a possible null pointer dereference: rg_old_tabs [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:3907:27: note: Assuming allocation function fails
Rsubread/src/readSummary.c:3907:27: note: Assignment 'rg_old_tabs=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/readSummary.c:3927:29: note: Null pointer dereference
Rsubread/src/readSummary.c:3928:40: warning: If memory allocation fails, then there is a possible null pointer dereference: rg_old_tabs [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:3907:27: note: Assuming allocation function fails
Rsubread/src/readSummary.c:3907:27: note: Assignment 'rg_old_tabs=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/readSummary.c:3928:40: note: Null pointer dereference
Rsubread/src/readSummary.c:3929:32: warning: If memory allocation fails, then there is a possible null pointer dereference: rg_old_tabs [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:3907:27: note: Assuming allocation function fails
Rsubread/src/readSummary.c:3907:27: note: Assignment 'rg_old_tabs=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/readSummary.c:3929:32: note: Null pointer dereference
Rsubread/src/readSummary.c:3930:33: warning: If memory allocation fails, then there is a possible null pointer dereference: rg_old_tabs [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:3907:27: note: Assuming allocation function fails
Rsubread/src/readSummary.c:3907:27: note: Assignment 'rg_old_tabs=malloc(sizeof(char*)*4)', assigned value is 0
Rsubread/src/readSummary.c:3930:33: note: Null pointer dereference
Rsubread/src/readSummary.c:4041:13: warning: If memory allocation fails, then there is a possible null pointer dereference: new_key [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4040:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4040:29: note: Assignment 'new_key=malloc(strlen(junckey)+1)', assigned value is 0
Rsubread/src/readSummary.c:4041:13: note: Null pointer dereference
Rsubread/src/readSummary.c:4057:13: warning: If memory allocation fails, then there is a possible null pointer dereference: new_key [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4056:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4056:29: note: Assignment 'new_key=malloc(strlen(junckey)+1)', assigned value is 0
Rsubread/src/readSummary.c:4057:13: note: Null pointer dereference
Rsubread/src/readSummary.c:4572:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4561:43: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4561:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),genes)', assigned value is 0
Rsubread/src/readSummary.c:4572:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4579:34: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4561:43: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4561:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),genes)', assigned value is 0
Rsubread/src/readSummary.c:4579:34: note: Null pointer dereference
Rsubread/src/readSummary.c:4581:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4561:43: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4561:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),genes)', assigned value is 0
Rsubread/src/readSummary.c:4581:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4588:24: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_number [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4561:43: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4561:43: note: Assignment 'gene_exons_number=calloc(sizeof(unsigned int),genes)', assigned value is 0
Rsubread/src/readSummary.c:4588:24: note: Null pointer dereference
Rsubread/src/readSummary.c:4588:53: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_pointer [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4562:44: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4562:44: note: Assignment 'gene_exons_pointer=calloc(sizeof(unsigned int),genes)', assigned value is 0
Rsubread/src/readSummary.c:4588:53: note: Null pointer dereference
Rsubread/src/readSummary.c:4590:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_chr [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4565:33: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4565:33: note: Assignment 'gene_exons_chr=malloc(sizeof(char*)*features)', assigned value is 0
Rsubread/src/readSummary.c:4590:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4591:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_start [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4563:42: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4563:42: note: Assignment 'gene_exons_start=malloc(sizeof(unsigned int)*features)', assigned value is 0
Rsubread/src/readSummary.c:4591:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4592:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_end [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4564:40: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4564:40: note: Assignment 'gene_exons_end=malloc(sizeof(unsigned int)*features)', assigned value is 0
Rsubread/src/readSummary.c:4592:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4593:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_strand [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4567:35: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4567:35: note: Assignment 'gene_exons_strand=malloc(features)', assigned value is 0
Rsubread/src/readSummary.c:4593:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4596:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_exons_pointer [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4562:44: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4562:44: note: Assignment 'gene_exons_pointer=calloc(sizeof(unsigned int),genes)', assigned value is 0
Rsubread/src/readSummary.c:4596:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4640:10: warning: If memory allocation fails, then there is a possible null pointer dereference: is_occupied [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4611:28: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4611:28: note: Assignment 'is_occupied=malloc(longest_gene_exons)', assigned value is 0
Rsubread/src/readSummary.c:4640:10: note: Null pointer dereference
Rsubread/src/readSummary.c:4645:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_chr_list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4616:30: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4616:30: note: Assignment 'out_chr_list=malloc(longest_gene_exons*(1+global_context->longest_chro_name)+1)', assigned value is 0
Rsubread/src/readSummary.c:4645:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4646:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_start_list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4617:32: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4617:32: note: Assignment 'out_start_list=malloc(11*longest_gene_exons+1)', assigned value is 0
Rsubread/src/readSummary.c:4646:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4647:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_end_list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4618:30: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4618:30: note: Assignment 'out_end_list=malloc(11*longest_gene_exons+1)', assigned value is 0
Rsubread/src/readSummary.c:4647:3: note: Null pointer dereference
Rsubread/src/readSummary.c:4648:3: warning: If memory allocation fails, then there is a possible null pointer dereference: out_strand_list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:4619:33: note: Assuming allocation function fails
Rsubread/src/readSummary.c:4619:33: note: Assignment 'out_strand_list=malloc(2*longest_gene_exons+1)', assigned value is 0
Rsubread/src/readSummary.c:4648:3: note: Null pointer dereference
Rsubread/src/readSummary.c:5351:4: warning: If memory allocation fails, then there is a possible null pointer dereference: key_list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:5342:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5342:19: note: Assignment 'key_list=malloc(sizeof(char*)*merged_junction_table->numOfElements)', assigned value is 0
Rsubread/src/readSummary.c:5351:4: note: Null pointer dereference
Rsubread/src/readSummary.c:5373:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
Rsubread/src/readSummary.c:5370:20: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5370:20: note: Assignment 'ofp=fopen(outfname,"w")', assigned value is 0
Rsubread/src/readSummary.c:5373:10: note: Null pointer dereference
Rsubread/src/readSummary.c:5378:11: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
Rsubread/src/readSummary.c:5370:20: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5370:20: note: Assignment 'ofp=fopen(outfname,"w")', assigned value is 0
Rsubread/src/readSummary.c:5378:11: note: Null pointer dereference
Rsubread/src/readSummary.c:5380:10: warning: If resource allocation fails, then there is a possible null pointer dereference: ofp [nullPointerOutOfResources]
Rsubread/src/readSummary.c:5370:20: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5370:20: note: Assignment 'ofp=fopen(outfname,"w")', assigned value is 0
Rsubread/src/readSummary.c:5380:10: note: Null pointer dereference
Rsubread/src/readSummary.c:5387:33: warning: If memory allocation fails, then there is a possible null pointer dereference: key_list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:5342:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5342:19: note: Assignment 'key_list=malloc(sizeof(char*)*merged_junction_table->numOfElements)', assigned value is 0
Rsubread/src/readSummary.c:5387:33: note: Null pointer dereference
Rsubread/src/readSummary.c:5419:3: warning: If memory allocation fails, then there is a possible null pointer dereference: gene_names [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:5362:28: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5362:28: note: Assignment 'gene_names=malloc(max_junction_genes*256)', assigned value is 0
Rsubread/src/readSummary.c:5419:3: note: Null pointer dereference
Rsubread/src/readSummary.c:5429:69: warning: If memory allocation fails, then there is a possible null pointer dereference: ret_juncs_small [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:5363:48: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5363:48: note: Assignment 'ret_juncs_small=malloc(sizeof(struct fc_junction_gene_t*)*max_junction_genes)', assigned value is 0
Rsubread/src/readSummary.c:5429:69: note: Null pointer dereference
Rsubread/src/readSummary.c:5429:93: warning: If memory allocation fails, then there is a possible null pointer dereference: ret_juncs_large [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:5364:48: note: Assuming allocation function fails
Rsubread/src/readSummary.c:5364:48: note: Assignment 'ret_juncs_large=malloc(sizeof(struct fc_junction_gene_t*)*max_junction_genes)', assigned value is 0
Rsubread/src/readSummary.c:5429:93: note: Null pointer dereference
Rsubread/src/readSummary.c:6262:6: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6262:6: note: Null pointer dereference
Rsubread/src/readSummary.c:6263:6: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6263:6: note: Null pointer dereference
Rsubread/src/readSummary.c:6264:6: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6264:6: note: Null pointer dereference
Rsubread/src/readSummary.c:6264:46: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6264:46: note: Null pointer dereference
Rsubread/src/readSummary.c:6266:13: warning: If memory allocation fails, then there is a possible null pointer dereference: mem_bucket_key [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6265:36: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6265:36: note: Assignment 'mem_bucket_key=malloc(strlen(bucket_key)+1)', assigned value is 0
Rsubread/src/readSummary.c:6266:13: note: Null pointer dereference
Rsubread/src/readSummary.c:6270:8: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6270:8: note: Null pointer dereference
Rsubread/src/readSummary.c:6270:26: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6270:26: note: Null pointer dereference
Rsubread/src/readSummary.c:6274:5: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6274:5: note: Null pointer dereference
Rsubread/src/readSummary.c:6274:19: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
Rsubread/src/readSummary.c:6274:19: note: Null pointer dereference
Rsubread/src/readSummary.c:6425:2: warning: If memory allocation fails, then there is a possible null pointer dereference: very_long_file_names [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6424:31: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6424:31: note: Assignment 'very_long_file_names=malloc(very_long_file_names_size)', assigned value is 0
Rsubread/src/readSummary.c:6425:2: note: Null pointer dereference
Rsubread/src/readSummary.c:6426:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fasta_contigs_name [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6361:36: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6361:36: note: Assignment 'fasta_contigs_name=malloc(1000)', assigned value is 0
Rsubread/src/readSummary.c:6426:2: note: Null pointer dereference
Rsubread/src/readSummary.c:6430:2: warning: If memory allocation fails, then there is a possible null pointer dereference: alias_file_name [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6362:33: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6362:33: note: Assignment 'alias_file_name=malloc(1000)', assigned value is 0
Rsubread/src/readSummary.c:6430:2: note: Null pointer dereference
Rsubread/src/readSummary.c:6437:18: warning: If memory allocation fails, then there is a possible null pointer dereference: out_name [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6360:26: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6360:26: note: Assignment 'out_name=malloc(1000)', assigned value is 0
Rsubread/src/readSummary.c:6437:18: note: Null pointer dereference
Rsubread/src/readSummary.c:6437:32: warning: If memory allocation fails, then there is a possible null pointer dereference: Rpath [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6363:23: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6363:23: note: Assignment 'Rpath=malloc(1000)', assigned value is 0
Rsubread/src/readSummary.c:6437:32: note: Null pointer dereference
Rsubread/src/readSummary.c:6440:2: warning: If memory allocation fails, then there is a possible null pointer dereference: cmd_rebuilt [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6366:29: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6366:29: note: Assignment 'cmd_rebuilt=malloc(cmd_rebuilt_size)', assigned value is 0
Rsubread/src/readSummary.c:6440:2: note: Null pointer dereference
Rsubread/src/readSummary.c:6556:16: warning: If memory allocation fails, then there is a possible null pointer dereference: Strand_Sensitive_Str [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6554:34: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6554:34: note: Assignment 'Strand_Sensitive_Str=strdup(optarg)', assigned value is 0
Rsubread/src/readSummary.c:6556:16: note: Null pointer dereference
Rsubread/src/readSummary.c:6556:57: warning: If memory allocation fails, then there is a possible null pointer dereference: Strand_Sensitive_Str [nullPointerOutOfMemory]
Rsubread/src/readSummary.c:6554:34: note: Assuming allocation function fails
Rsubread/src/readSummary.c:6554:34: note: Assignment 'Strand_Sensitive_Str=strdup(optarg)', assigned value is 0
Rsubread/src/readSummary.c:6556:57: note: Null pointer dereference
Rsubread/src/readSummary.c:2259:16: style:inconclusive: Same expression used in consecutive assignments of 'chro_cursor' and 'section_start_chro'. [duplicateAssignExpression]
Rsubread/src/readSummary.c:2259:38: note: Same expression used in consecutive assignments of 'chro_cursor' and 'section_start_chro'.
Rsubread/src/readSummary.c:2259:16: note: Same expression used in consecutive assignments of 'chro_cursor' and 'section_start_chro'.
Rsubread/src/readSummary.c:2733:9: style: The comparison 'ret < 1' is always false. [knownConditionTrueFalse]
Rsubread/src/readSummary.c:2697:12: note: 'ret' is assigned value '1' here.
Rsubread/src/readSummary.c:2733:9: note: The comparison 'ret < 1' is always false.
Rsubread/src/readSummary.c:5489:18: style: Variable 'gene_name_tail' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/readSummary.c:5418:18: note: gene_name_tail is assigned
Rsubread/src/readSummary.c:5489:18: note: gene_name_tail is overwritten
Rsubread/src/readSummary.c:6845:12: style: Variable 'Rargv[54]' is reassigned a value before the old one has been used. [redundantAssignment]
Rsubread/src/readSummary.c:6844:12: note: Rargv[54] is assigned
Rsubread/src/readSummary.c:6845:12: note: Rargv[54] is overwritten
Rsubread/src/readSummary.c:821:2: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode]
Rsubread/src/readSummary.c:6297:418: style:inconclusive: Function 'readSummary_single_file' argument 16 names different: declaration 'junc_glob_tab' definition 'junction_global_table'. [funcArgNamesDifferent]
Rsubread/src/readSummary.c:5536:418: note: Function 'readSummary_single_file' argument 16 names different: declaration 'junc_glob_tab' definition 'junction_global_table'.
Rsubread/src/readSummary.c:6297:418: note: Function 'readSummary_single_file' argument 16 names different: declaration 'junc_glob_tab' definition 'junction_global_table'.
Rsubread/src/readSummary.c:6297:453: style:inconclusive: Function 'readSummary_single_file' argument 17 names different: declaration 'splicing_glob_tab' definition 'splicing_global_table'. [funcArgNamesDifferent]
Rsubread/src/readSummary.c:5536:445: note: Function 'readSummary_single_file' argument 17 names different: declaration 'splicing_glob_tab' definition 'splicing_global_table'.
Rsubread/src/readSummary.c:6297:453: note: Function 'readSummary_single_file' argument 17 names different: declaration 'splicing_glob_tab' definition 'splicing_global_table'.
Rsubread/src/readSummary.c:466:7: style: Local variable 'nch' shadows outer variable [shadowVariable]
Rsubread/src/readSummary.c:403:24: note: Shadowed declaration
Rsubread/src/readSummary.c:466:7: note: Shadow variable
Rsubread/src/readSummary.c:1904:8: style: Local variable 'thread_no' shadows outer argument [shadowArgument]
Rsubread/src/readSummary.c:1834:50: note: Shadowed declaration
Rsubread/src/readSummary.c:1904:8: note: Shadow variable
Rsubread/src/readSummary.c:3958:23: style: Local variable 'cursor' shadows outer variable [shadowVariable]
Rsubread/src/readSummary.c:3901:19: note: Shadowed declaration
Rsubread/src/readSummary.c:3958:23: note: Shadow variable
Rsubread/src/readSummary.c:3974:23: style: Local variable 'cursor' shadows outer variable [shadowVariable]
Rsubread/src/readSummary.c:3901:19: note: Shadowed declaration
Rsubread/src/readSummary.c:3974:23: note: Shadow variable
Rsubread/src/readSummary.c:340:29: style: Parameter 'chroname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:340:45: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:396:60: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:396:93: style: Parameter 'chroname' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:396:128: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:396:143: style: Parameter 'extra_tags' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:575:73: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:809:52: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:809:75: style: Parameter 'out' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:835:79: style: Parameter 'feature_name' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:835:100: style: Parameter 'chro' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:868:38: style: Parameter 'infile' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:868:53: style: Parameter 'needed' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:872:9: style: Variable 't1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:882:54: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:1063:11: style: Variable 'start_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:1064:11: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:1102:11: style: Variable 'strand_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:1163:12: style: Variable 'start_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:1164:12: style: Variable 'end_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:1191:12: style: Variable 'strand_str' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:1419:13: style: Variable 'ret_start' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:1644:25: style: Parameter 's1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:1644:36: style: Parameter 's2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:1657:76: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:1680:33: style: Parameter 'rl' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:1815:33: style: Parameter 'n' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:2258:9: style: Variable 'cigar_opt_ints' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:2413:137: style: Parameter 'Starting_Chro_Points_1BASE' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:2413:221: style: Parameter 'Section_Lengths' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:2413:264: style: Parameter 'Event_After_Section' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:2476:52: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:2538:30: style: Parameter 'oldbin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:2538:74: style: Parameter 'types' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:2673:128: style: Parameter 'bin' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:3162:14: style: Variable 'anno_chro_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3331:37: style: Parameter 'x1_bitmap' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:3381:10: style: Variable 'count_ptr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3392:11: style: Variable 'lr_key' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3401:17: style: Variable 'pos' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3416:155: style: Parameter 'start_poses' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:3416:185: style: Parameter 'lens' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:3538:17: style: Variable 'hits_indices_X1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3539:13: style: Variable 'used_hit_X1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3569:19: style: Variable 'hits_indices_X2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3609:16: style: Variable 'hits_indices_X1' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3638:18: style: Variable 'hits_indices_X2' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3679:16: style: Variable 'hits_indices' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3841:15: style: Variable 'final_feture_name' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3932:17: style: Variable 'rg_thread_counts' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3933:25: style: Variable 'rg_thread_sum_reads' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3963:16: style: Variable 'new_key' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3979:16: style: Variable 'new_key' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4037:13: style: Variable 'junckey' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4054:13: style: Variable 'junckey' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4109:47: style: Parameter 'out' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4110:9: style: Variable 'slash' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4119:62: style: Parameter 'global_context' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4119:85: style: Parameter 'in_fnames' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4157:376: style: Parameter 'feature_name_column' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4157:404: style: Parameter 'gene_id_column' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4157:969: style: Parameter 'temp_dir' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4157:1223: style: Parameter 'Rpath' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4157:1265: style: Parameter 'annotation_file_screen_output' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4520:36: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:4554:10: style: Variable 'next_fn' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4604:15: style: Variable 'this_col' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4625:10: style: Variable 'tnamep' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4724:10: style: Variable 'QCcontent' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4725:10: style: Variable 'QCtab' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4799:10: style: Variable 'next_fn' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4804:9: style: Variable 'keys' can be declared as const array [constVariable]
Rsubread/src/readSummary.c:4812:15: style: Variable 'cntr' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4853:9: style: Variable 'next_fn' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:4870:15: style: Variable 'this_list' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5282:34: style: Parameter 'j1' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:5282:59: style: Parameter 'j2' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:5314:12: style: Variable 'ky' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5332:12: style: Variable 'ky' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5377:10: style: Variable 'next_fn' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5398:10: style: Variable 'strand' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5468:24: style: Variable 'primary_gene' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5505:16: style: Variable 'junc_table' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5538:45: style: Parameter 'fnames' can be declared as pointer to const [constParameterPointer]
Rsubread/src/readSummary.c:5982:11: style: Variable 'short_loop_fname' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:5995:9: style: Variable 'next_strand_mode' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:6384:9: style: Variable 'old_zero_smode' can be declared as pointer to const [constVariablePointer]
Rsubread/src/readSummary.c:3965:17: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/readSummary.c:3983:17: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/readSummary.c:4042:14: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/readSummary.c:4062:14: portability: 'globval' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
Rsubread/src/readSummary.c:3554:55: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
Rsubread/src/readSummary.c:3742:49: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
Rsubread/src/readSummary.c:629:18: style: Variable 'nNonExistFiles' is assigned a value that is never used. [unreadVariable]
Rsubread/src/readSummary.c:1143:21: style: Variable 'is_gene_id_found' is assigned a value that is never used. [unreadVariable]
Rsubread/src/readSummary.c:1521:35: style: Variable 'sort_i' is assigned a value that is never used. [unreadVariable]
Rsubread/src/readSummary.c:3819:41: style: Variable 'assignment_target_number' is assigned a value that is never used. [unreadVariable]
Rsubread/src/readSummary.c:3820:66: style: Variable 'assignment_target_number' is assigned a value that is never used. [unreadVariable]
Rsubread/src/readSummary.c:3889:25: style: Unused variable: sample_i [unusedVariable]
Rsubread/src/readSummary.c:6301:30: style: Variable 'line' is allocated memory that is never used. [unusedAllocatedMemory]
diff:
head Rsubread/src/cell-counts.c:1298:50: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
     Rsubread/src/cell-counts.c:1298:50: note: Null pointer dereference
head Rsubread/src/cell-counts.c:1299:53: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stub [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:1291:49: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:1291:49: note: Assignment 'chro_stub=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
     Rsubread/src/cell-counts.c:1299:53: note: Null pointer dereference
head Rsubread/src/cell-counts.c:3453:52: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:3453:52: note: Null pointer dereference
head Rsubread/src/cell-counts.c:3453:94: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:3453:94: note: Null pointer dereference
head Rsubread/src/cell-counts.c:3457:100: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:3457:100: note: Null pointer dereference
head Rsubread/src/cell-counts.c:3458:102: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:3458:102: note: Null pointer dereference
head Rsubread/src/cell-counts.c:3458:151: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:3458:151: note: Null pointer dereference
head Rsubread/src/cell-counts.c:3462:102: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4878:38: note: Calling function 'cellCounts_run_mapping', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:3459:19: note: Assuming condition is false
     Rsubread/src/cell-counts.c:3462:102: note: Null pointer dereference
head Rsubread/src/cell-counts.c:528:49: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4876:39: note: Calling function 'cellCounts_args_context', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:528:49: note: Null pointer dereference
head Rsubread/src/cell-counts.c:657:99: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:1399:42: note: Calling function 'determine_total_index_blocks', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:657:99: note: Null pointer dereference
2.17.0 Rsubread/src/cell-counts.c:738:30: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/cell-counts.c:722:25: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:722:25: note: Assignment 'outbuff=malloc(outcapa)', assigned value is 0
     Rsubread/src/cell-counts.c:725:13: note: Assuming condition is false
     Rsubread/src/cell-counts.c:738:30: note: Null pointer addition
head Rsubread/src/cell-counts.c:738:30: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/cell-counts.c:722:25: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:722:25: note: Assignment 'outbuff=malloc(outcapa)', assigned value is 0
     Rsubread/src/cell-counts.c:725:13: note: Assuming condition is false
     Rsubread/src/cell-counts.c:738:30: note: Null pointer addition
head Rsubread/src/cell-counts.c:810:68: warning: If memory allocation fails, then there is a possible null pointer dereference: cct_context [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:4872:44: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:4872:44: note: Assignment 'cct_context=calloc(sizeof(struct cellcounts_global_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:4877:39: note: Calling function 'cellCounts_load_context', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:1404:42: note: Calling function 'cellCounts_load_scRNA_tables', 1st argument 'cct_context' value is 0
     Rsubread/src/cell-counts.c:810:68: note: Null pointer dereference
head Rsubread/src/cell-counts.c:932:104: warning: If memory allocation fails, then there is a possible null pointer dereference: new_added [nullPointerOutOfMemory]
     Rsubread/src/cell-counts.c:910:40: note: Assuming allocation function fails
     Rsubread/src/cell-counts.c:910:40: note: Assignment 'new_added=calloc(sizeof(struct fc_feature_info_t),1)', assigned value is 0
     Rsubread/src/cell-counts.c:932:104: note: Null pointer dereference
head Rsubread/src/core-bigtable.c:287:31: warning: If memory allocation fails, then there is a possible null pointer dereference: had_items [nullPointerOutOfMemory]
     Rsubread/src/core-bigtable.c:274:22: note: Assuming allocation function fails
     Rsubread/src/core-bigtable.c:274:22: note: Assignment 'had_items=malloc(sizeof(struct bucketed_table_bucket_t))', assigned value is 0
     Rsubread/src/core-bigtable.c:287:31: note: Null pointer dereference
head Rsubread/src/core-indel.c:707:83: warning: If memory allocation fails, then there is a possible null pointer dereference: indel_thread_context [nullPointerOutOfMemory]
     Rsubread/src/core-indel.c:695:81: note: Assuming allocation function fails
     Rsubread/src/core-indel.c:695:50: note: Assignment 'indel_thread_context=(struct indel_thread_context_t*)malloc(sizeof(struct indel_thread_context_t))', assigned value is 0
     Rsubread/src/core-indel.c:707:83: note: Null pointer dereference
head Rsubread/src/core-junction.c:6190:41: error: Memory is allocated but not initialized: s2_ptrs [uninitdata]
head Rsubread/src/core-junction.c:6191:49: error: Memory is allocated but not initialized: s2_poses [uninitdata]
head Rsubread/src/core.c:892:54: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: global_context [nullPointerOutOfMemory]
     Rsubread/src/core.c:883:44: note: Assuming allocation function fails
     Rsubread/src/core.c:883:19: note: Assignment 'global_context=(struct global_context_t*)malloc(sizeof(struct global_context_t))', assigned value is 0
     Rsubread/src/core.c:892:54: note: Null pointer dereference
head Rsubread/src/detection-calls.c:305:25: warning: If memory allocation fails, then there is a possible null pointer dereference: gc_total_2int [nullPointerOutOfMemory]
     Rsubread/src/detection-calls.c:304:28: note: Assuming allocation function fails
     Rsubread/src/detection-calls.c:304:28: note: Assignment 'gc_total_2int=malloc(sizeof(int)*2)', assigned value is 0
     Rsubread/src/detection-calls.c:305:25: note: Null pointer dereference
head Rsubread/src/hashtable.c:94:45: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
     Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
     Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
     Rsubread/src/hashtable.c:94:45: note: Null pointer dereference
head Rsubread/src/hashtable.c:95:64: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
     Rsubread/src/hashtable.c:90:26: note: Assuming allocation function fails
     Rsubread/src/hashtable.c:90:26: note: Assignment 'ret=malloc(sizeof(struct ArrayList))', assigned value is 0
     Rsubread/src/hashtable.c:95:64: note: Null pointer dereference
head Rsubread/src/input-blc.c:1540:37: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
     Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
     Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
     Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
     Rsubread/src/input-blc.c:1688:27: note: Calling function 'scBAM_inner_fopen', 1st argument 'bam_input' value is 0
     Rsubread/src/input-blc.c:1540:37: note: Null pointer dereference
head Rsubread/src/input-blc.c:1540:65: warning: If memory allocation fails, then there is a possible null pointer dereference: bam_input [nullPointerOutOfMemory]
     Rsubread/src/input-blc.c:1258:38: note: Assuming allocation function fails
     Rsubread/src/input-blc.c:1258:38: note: Assignment 'scBAM_input=malloc(sizeof(struct input_scBAM_t))', assigned value is 0
     Rsubread/src/input-blc.c:1259:29: note: Calling function 'input_scBAM_init', 1st argument 'scBAM_input' value is 0
     Rsubread/src/input-blc.c:1688:27: note: Calling function 'scBAM_inner_fopen', 1st argument 'bam_input' value is 0
     Rsubread/src/input-blc.c:1540:65: note: Null pointer dereference
head Rsubread/src/input-blc.c:580:17: style: Variable 'npos' is assigned a value that is never used. [unreadVariable]
2.17.0 Rsubread/src/input-blc.c:665:25: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-blc.c:661:30: note: Assuming allocation function fails
     Rsubread/src/input-blc.c:661:30: note: Assignment 'threads=malloc(sizeof(pthread_t)*cache_input->all_threads)', assigned value is 0
     Rsubread/src/input-blc.c:665:25: note: Null pointer addition
head Rsubread/src/input-blc.c:665:25: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-blc.c:661:30: note: Assuming allocation function fails
     Rsubread/src/input-blc.c:661:30: note: Assignment 'threads=malloc(sizeof(pthread_t)*cache_input->all_threads)', assigned value is 0
     Rsubread/src/input-blc.c:665:25: note: Null pointer addition
2.17.0 Rsubread/src/input-files.c:3026:25: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:3023:34: note: Assuming allocation function fails
     Rsubread/src/input-files.c:3023:34: note: Assignment 'margin_data=malloc(thread_context->input_buff_BIN_used-thread_context->input_buff_BIN_ptr+4)', assigned value is 0
     Rsubread/src/input-files.c:3026:25: note: Null pointer addition
head Rsubread/src/input-files.c:3026:25: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:3023:34: note: Assuming allocation function fails
     Rsubread/src/input-files.c:3023:34: note: Assignment 'margin_data=malloc(thread_context->input_buff_BIN_used-thread_context->input_buff_BIN_ptr+4)', assigned value is 0
     Rsubread/src/input-files.c:3026:25: note: Null pointer addition
2.17.0 Rsubread/src/input-files.c:3165:20: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:3162:28: note: Assuming allocation function fails
     Rsubread/src/input-files.c:3162:28: note: Assignment 'header_sec=malloc(reflen+20)', assigned value is 0
     Rsubread/src/input-files.c:3165:20: note: Null pointer addition
head Rsubread/src/input-files.c:3165:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:3162:28: note: Assuming allocation function fails
     Rsubread/src/input-files.c:3162:28: note: Assignment 'header_sec=malloc(reflen+20)', assigned value is 0
     Rsubread/src/input-files.c:3165:20: note: Null pointer addition
2.17.0 Rsubread/src/input-files.c:3166:20: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:3162:28: note: Assuming allocation function fails
     Rsubread/src/input-files.c:3162:28: note: Assignment 'header_sec=malloc(reflen+20)', assigned value is 0
     Rsubread/src/input-files.c:3166:20: note: Null pointer addition
head Rsubread/src/input-files.c:3166:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:3162:28: note: Assuming allocation function fails
     Rsubread/src/input-files.c:3162:28: note: Assignment 'header_sec=malloc(reflen+20)', assigned value is 0
     Rsubread/src/input-files.c:3166:20: note: Null pointer addition
head Rsubread/src/input-files.c:3244:6: style: Variable 'seq_len' is assigned a value that is never used. [unreadVariable]
2.17.0 Rsubread/src/input-files.c:4282:63: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:4273:23: note: Assuming allocation function fails
     Rsubread/src/input-files.c:4273:23: note: Assignment 'names=malloc(orphant_fp_no*max_name_len)', assigned value is 0
     Rsubread/src/input-files.c:4282:63: note: Null pointer addition
head Rsubread/src/input-files.c:4282:63: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:4273:23: note: Assuming allocation function fails
     Rsubread/src/input-files.c:4273:23: note: Assignment 'names=malloc(orphant_fp_no*max_name_len)', assigned value is 0
     Rsubread/src/input-files.c:4282:63: note: Null pointer addition
2.17.0 Rsubread/src/input-files.c:4505:21: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:4503:30: note: Assuming allocation function fails
     Rsubread/src/input-files.c:4503:30: note: Assignment 'margin_data=malloc(save_start_pos+4)', assigned value is 0
     Rsubread/src/input-files.c:4505:21: note: Null pointer addition
head Rsubread/src/input-files.c:4505:21: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:4503:30: note: Assuming allocation function fails
     Rsubread/src/input-files.c:4503:30: note: Assignment 'margin_data=malloc(save_start_pos+4)', assigned value is 0
     Rsubread/src/input-files.c:4505:21: note: Null pointer addition
2.17.0 Rsubread/src/input-files.c:4608:12: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:4606:21: note: Assuming allocation function fails
     Rsubread/src/input-files.c:4606:21: note: Assignment 'tb=malloc(Elen+Slen)', assigned value is 0
     Rsubread/src/input-files.c:4608:12: note: Null pointer addition
head Rsubread/src/input-files.c:4608:12: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/input-files.c:4606:21: note: Assuming allocation function fails
     Rsubread/src/input-files.c:4606:21: note: Assignment 'tb=malloc(Elen+Slen)', assigned value is 0
     Rsubread/src/input-files.c:4608:12: note: Null pointer addition
head Rsubread/src/longread-mapping.c:1155:53: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
     Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
     Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
     Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
     Rsubread/src/longread-mapping.c:1184:59: note: Calling function 'LRMdo_dynamic_programming_read', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:1155:53: note: Null pointer dereference
head Rsubread/src/longread-mapping.c:1180:122: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
     Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
     Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
     Rsubread/src/longread-mapping.c:1180:122: note: Null pointer dereference
head Rsubread/src/longread-mapping.c:1180:152: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
     Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
     Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
     Rsubread/src/longread-mapping.c:1180:152: note: Null pointer dereference
2.17.0 Rsubread/src/longread-mapping.c:465:5: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
     Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
     Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
     Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
     Rsubread/src/longread-mapping.c:1183:50: note: Calling function 'LRMdo_one_voting_read', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:504:57: note: Calling function 'LRMdo_one_voting_read_single', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:490:48: note: Calling function 'LRMcalc_total_subreads', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:465:5: note: Null pointer dereference
2.17.0 Rsubread/src/longread-mapping.c:491:30: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
     Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
     Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
     Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
     Rsubread/src/longread-mapping.c:1183:50: note: Calling function 'LRMdo_one_voting_read', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:504:57: note: Calling function 'LRMdo_one_voting_read_single', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:491:30: note: Null pointer dereference
2.17.0 Rsubread/src/longread-mapping.c:503:6: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
     Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
     Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
     Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
     Rsubread/src/longread-mapping.c:1183:50: note: Calling function 'LRMdo_one_voting_read', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:503:6: note: Null pointer dereference
2.17.0 Rsubread/src/longread-mapping.c:505:11: warning: If memory allocation fails, then there is a possible null pointer dereference: iteration_context [nullPointerOutOfMemory]
     Rsubread/src/longread-mapping.c:1176:28: note: Assuming allocation function fails
     Rsubread/src/longread-mapping.c:1176:28: note: Assignment 'iteration_context=malloc(sizeof(struct LRMread_iteration_context_t))', assigned value is 0
     Rsubread/src/longread-mapping.c:1181:6: note: Assuming condition is false
     Rsubread/src/longread-mapping.c:1183:50: note: Calling function 'LRMdo_one_voting_read', 3rd argument 'iteration_context' value is 0
     Rsubread/src/longread-mapping.c:505:11: note: Null pointer dereference
head Rsubread/src/processExons.c:93:6: style: Variable 'gene' is assigned a value that is never used. [unreadVariable]
head Rsubread/src/readSummary.c:1130:54: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
     Rsubread/src/readSummary.c:1130:54: note: Null pointer dereference
head Rsubread/src/readSummary.c:1135:45: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:1126:23: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:1126:23: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
     Rsubread/src/readSummary.c:1135:45: note: Null pointer dereference
head Rsubread/src/readSummary.c:1276:55: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
     Rsubread/src/readSummary.c:1276:55: note: Null pointer dereference
head Rsubread/src/readSummary.c:1281:46: warning: If memory allocation fails, then there is a possible null pointer dereference: chro_stab [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:1272:24: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:1272:24: note: Assignment 'chro_stab=calloc(sizeof(struct fc_chromosome_index_info),1)', assigned value is 0
     Rsubread/src/readSummary.c:1281:46: note: Null pointer dereference
head Rsubread/src/readSummary.c:6264:46: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
     Rsubread/src/readSummary.c:6264:46: note: Null pointer dereference
head Rsubread/src/readSummary.c:6270:26: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
     Rsubread/src/readSummary.c:6270:26: note: Null pointer dereference
head Rsubread/src/readSummary.c:6274:19: warning: If memory allocation fails, then there is a possible null pointer dereference: list [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:6261:19: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:6261:19: note: Assignment 'list=malloc(sizeof(struct gene_info_list_t))', assigned value is 0
     Rsubread/src/readSummary.c:6274:19: note: Null pointer dereference
head Rsubread/src/readSummary.c:6556:57: warning: If memory allocation fails, then there is a possible null pointer dereference: Strand_Sensitive_Str [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:6554:34: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:6554:34: note: Assignment 'Strand_Sensitive_Str=strdup(optarg)', assigned value is 0
     Rsubread/src/readSummary.c:6556:57: note: Null pointer dereference
head Rsubread/src/readSummary.c:698:21: warning: If memory allocation fails, then there is a possible null pointer dereference: PEexpectStr [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:681:29: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:681:29: note: Assignment 'PEexpectStr=malloc(nfiles*6)', assigned value is 0
     Rsubread/src/readSummary.c:698:21: note: Null pointer dereference
head Rsubread/src/readSummary.c:711:21: warning: If memory allocation fails, then there is a possible null pointer dereference: PEassignStr [nullPointerOutOfMemory]
     Rsubread/src/readSummary.c:680:29: note: Assuming allocation function fails
     Rsubread/src/readSummary.c:680:29: note: Assignment 'PEassignStr=malloc(nfiles*6)', assigned value is 0
     Rsubread/src/readSummary.c:711:21: note: Null pointer dereference
2.17.0 Rsubread/src/sambam-file.c:1851:20: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/sambam-file.c:1849:29: note: Assuming allocation function fails
     Rsubread/src/sambam-file.c:1849:29: note: Assignment 'key_binpos=malloc(12)', assigned value is 0
     Rsubread/src/sambam-file.c:1851:20: note: Null pointer addition
head Rsubread/src/sambam-file.c:1851:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/sambam-file.c:1849:29: note: Assuming allocation function fails
     Rsubread/src/sambam-file.c:1849:29: note: Assignment 'key_binpos=malloc(12)', assigned value is 0
     Rsubread/src/sambam-file.c:1851:20: note: Null pointer addition
2.17.0 Rsubread/src/sambam-file.c:1852:20: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/sambam-file.c:1849:29: note: Assuming allocation function fails
     Rsubread/src/sambam-file.c:1849:29: note: Assignment 'key_binpos=malloc(12)', assigned value is 0
     Rsubread/src/sambam-file.c:1852:20: note: Null pointer addition
head Rsubread/src/sambam-file.c:1852:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     Rsubread/src/sambam-file.c:1849:29: note: Assuming allocation function fails
     Rsubread/src/sambam-file.c:1849:29: note: Assignment 'key_binpos=malloc(12)', assigned value is 0
     Rsubread/src/sambam-file.c:1852:20: note: Null pointer addition
head Rsubread/src/sambam-file.c:2105:56: warning: If memory allocation fails, then there is a possible null pointer dereference: current_min_fps [nullPointerOutOfMemory]
     Rsubread/src/sambam-file.c:2094:49: note: Assuming allocation function fails
     Rsubread/src/sambam-file.c:2094:49: note: Assignment 'current_min_fps=malloc(sizeof(unsigned long long)*this_size)', assigned value is 0
     Rsubread/src/sambam-file.c:2105:56: note: Null pointer dereference
head Rsubread/src/sambam-file.c:2588:24: warning: If memory allocation fails, then there is a possible null pointer dereference: writer [nullPointerOutOfMemory]
     Rsubread/src/sambam-file.c:2610:34: note: Assuming allocation function fails
     Rsubread/src/sambam-file.c:2610:34: note: Assignment 'ret=calloc(sizeof(struct simple_bam_writer),1)', assigned value is 0
     Rsubread/src/sambam-file.c:2613:31: note: Calling function 'simple_bam_write', 3rd argument 'ret' value is 0
     Rsubread/src/sambam-file.c:2588:24: note: Null pointer dereference


DONE