2025-05-05 10:23 ftp://ftp.de.debian.org/debian/pool/main/l/lagan/lagan_2.0.orig.tar.gz cppcheck-options: --library=posix --library=gnu --library=bsd --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: c79862b (2025-05-05 10:59:17 +0200) count: 990 927 elapsed-time: 2.5 2.5 head-timing-info: old-timing-info: head results: lagan20/src/anchors.c:74:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] lagan20/src/ancseqrest.cpp:51:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/ancseqrest.cpp:68:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/ancseqrest.cpp:77:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/ancseqrest.cpp:200:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] lagan20/src/ancseqrest.cpp:66:22: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] lagan20/src/ancseqrest.cpp:75:22: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] lagan20/src/ancseqrest.cpp:118:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/ancseqrest.cpp:244:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/ancseqrest.cpp:265:8: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseqrest.cpp:264:25: note: Assuming allocation function fails lagan20/src/ancseqrest.cpp:264:12: note: Assignment 'buf=(char*)std::malloc(length*sizeof(char))', assigned value is 0 lagan20/src/ancseqrest.cpp:265:8: note: Null pointer dereference lagan20/src/ancseqrest.cpp:264:12: style: C-style pointer casting [cstyleCast] lagan20/src/ancseqrest.cpp:48:23: performance: Function parameter 'path' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:133:37: performance: Function parameter 'header' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:151:37: performance: Function parameter 'header' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:198:48: performance: Function parameter 'ancestor' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:198:104: performance: Function parameter 'descSeqName' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:198:145: performance: Function parameter 'desc1' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:198:158: performance: Function parameter 'desc2' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:252:29: performance: Function parameter 'genomePath' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:269:27: performance: Function parameter 'seqName' should be passed by const reference. [passedByValue] lagan20/src/ancseqrest.cpp:48:34: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseqrest.cpp:57:17: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseqrest.cpp:57:37: style: Parameter 'argv' can be declared as const array [constParameter] lagan20/src/ancseqrest.cpp:64:21: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseqrest.cpp:73:23: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseqrest.cpp:247:11: warning: Uninitialized variables: record.offset, record.length [uninitvar] lagan20/src/ancseqrest.cpp:243:18: note: Assuming condition is false lagan20/src/ancseqrest.cpp:247:11: note: Uninitialized variables: record.offset, record.length lagan20/src/ancseqrest.cpp:247:11: error: Uninitialized struct member: record.offset [uninitStructMember] lagan20/src/ancseqrest.cpp:247:11: error: Uninitialized struct member: record.length [uninitStructMember] lagan20/src/util.cpp:19:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/util.cpp:36:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/util.cpp:45:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/ancseqrest.cpp:111:6: style: Unused variable: tmp [unusedVariable] lagan20/src/ancseqrest.cpp:173:12: style: Variable 'prev.start' is assigned a value that is never used. [unreadVariable] lagan20/src/anchors.c:99:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:99:5: note: Null pointer dereference lagan20/src/anchors.c:100:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:100:5: note: Null pointer dereference lagan20/src/anchors.c:101:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:101:5: note: Null pointer dereference lagan20/src/anchors.c:102:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:102:5: note: Null pointer dereference lagan20/src/anchors.c:103:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:103:5: note: Null pointer dereference lagan20/src/anchors.c:104:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:104:5: note: Null pointer dereference lagan20/src/anchors.c:107:9: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:107:9: note: Null pointer dereference lagan20/src/anchors.c:130:9: warning: If memory allocation fails, then there is a possible null pointer dereference: array [nullPointerOutOfMemory] lagan20/src/anchors.c:96:27: note: Assuming allocation function fails lagan20/src/anchors.c:96:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/anchors.c:108:24: note: Calling function 'findBestChain', 1st argument 'myptrs' value is 0 lagan20/src/anchors.c:130:9: note: Null pointer dereference lagan20/src/anchors.c:260:2: warning: If memory allocation fails, then there is a possible null pointer dereference: temp [nullPointerOutOfMemory] lagan20/src/anchors.c:259:22: note: Assuming allocation function fails lagan20/src/anchors.c:259:9: note: Assignment 'temp=(struct gfc*)malloc(sizeof(struct gfc))', assigned value is 0 lagan20/src/anchors.c:260:2: note: Null pointer dereference lagan20/src/anchors.c:124:26: style:inconclusive: Function 'findBestChain' argument 1 names different: declaration 'myarr' definition 'array'. [funcArgNamesDifferent] lagan20/src/anchors.c:40:26: note: Function 'findBestChain' argument 1 names different: declaration 'myarr' definition 'array'. lagan20/src/anchors.c:124:26: note: Function 'findBestChain' argument 1 names different: declaration 'myarr' definition 'array'. lagan20/src/anchors.c:167:20: style:inconclusive: Function 'doOutput' argument 1 names different: declaration 'mylist' definition 'best'. [funcArgNamesDifferent] lagan20/src/anchors.c:41:20: note: Function 'doOutput' argument 1 names different: declaration 'mylist' definition 'best'. lagan20/src/anchors.c:167:20: note: Function 'doOutput' argument 1 names different: declaration 'mylist' definition 'best'. lagan20/src/anchors.c:245:36: style:inconclusive: Function 'parseCHAOS' argument 2 names different: declaration 'numhits' definition 'totnum'. [funcArgNamesDifferent] lagan20/src/anchors.c:39:36: note: Function 'parseCHAOS' argument 2 names different: declaration 'numhits' definition 'totnum'. lagan20/src/anchors.c:245:36: note: Function 'parseCHAOS' argument 2 names different: declaration 'numhits' definition 'totnum'. lagan20/src/anchors.c:113:18: style: Parameter 'one' can be declared as pointer to const [constParameterPointer] lagan20/src/anchors.c:113:28: style: Parameter 'two' can be declared as pointer to const [constParameterPointer] lagan20/src/anchors.c:118:19: style: Parameter 'next' can be declared as pointer to const [constParameterPointer] lagan20/src/anchors.c:118:30: style: Parameter 'prev' can be declared as pointer to const [constParameterPointer] lagan20/src/anchors.c:164:16: warning: Uninitialized variable: bestptr [uninitvar] lagan20/src/anchors.c:156:10: note: Assuming condition is false lagan20/src/anchors.c:164:16: note: Uninitialized variable: bestptr lagan20/src/anchors.c:49:10: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] lagan20/src/anchors.c:49:7: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] lagan20/src/anchors.c:171:26: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/anchors.c:178:9: style: Variable 'len' is assigned a value that is never used. [unreadVariable] lagan20/src/anchors.c:171:14: style: Unused variable: i [unusedVariable] lagan20/src/anchors.c:171:17: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/diagmatrix.c:118:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/diagmatrix.c:160:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/diagmatrix.c:201:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/diagmatrix.c:246:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dirty [valueFlowBailoutIncompleteVar] lagan20/src/diagmatrix.c:318:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/diagmatrix.c:327:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/util.cpp:34:22: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] lagan20/src/util.cpp:43:22: style: Array index 'i' is used before limits check. [arrayIndexThenCheck] lagan20/src/faindex.cpp:23:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/cutmfa.cpp:130:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/faindex.cpp:43:8: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory] lagan20/src/faindex.cpp:42:25: note: Assuming allocation function fails lagan20/src/faindex.cpp:42:12: note: Assignment 'seq=(char*)std::malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/faindex.cpp:43:8: note: Null pointer dereference lagan20/src/faindex.cpp:54:8: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory] lagan20/src/faindex.cpp:53:25: note: Assuming allocation function fails lagan20/src/faindex.cpp:53:12: note: Assignment 'seq=(char*)std::malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/faindex.cpp:54:8: note: Null pointer dereference lagan20/src/faindex.cpp:42:12: style: C-style pointer casting [cstyleCast] lagan20/src/faindex.cpp:53:12: style: C-style pointer casting [cstyleCast] lagan20/src/util.cpp:16:23: performance: Function parameter 'path' should be passed by const reference. [passedByValue] lagan20/src/faindex.cpp:29:42: performance: Function parameter 'path' should be passed by const reference. [passedByValue] lagan20/src/faindex.cpp:39:45: performance: Function parameter 'seqId' should be passed by const reference. [passedByValue] lagan20/src/faindex.cpp:47:46: performance: Function parameter 'seqId' should be passed by const reference. [passedByValue] lagan20/src/cutmfa.cpp:57:37: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] lagan20/src/cutmfa.cpp:74:38: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] lagan20/src/util.cpp:16:34: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer] lagan20/src/util.cpp:25:17: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] lagan20/src/util.cpp:25:37: style: Parameter 'argv' can be declared as const array [constParameter] lagan20/src/util.cpp:32:21: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] lagan20/src/util.cpp:41:23: style: Parameter 'key' can be declared as pointer to const [constParameterPointer] lagan20/src/faindex.cpp:26:11: warning: Uninitialized variables: record.offset, record.length [uninitvar] lagan20/src/faindex.cpp:22:18: note: Assuming condition is false lagan20/src/faindex.cpp:26:11: note: Uninitialized variables: record.offset, record.length lagan20/src/faindex.cpp:26:11: error: Uninitialized struct member: record.offset [uninitStructMember] lagan20/src/faindex.cpp:26:11: error: Uninitialized struct member: record.length [uninitStructMember] lagan20/src/cutmfa.cpp:104:6: style: Variable 'count' is assigned a value that is never used. [unreadVariable] lagan20/src/faindex.cpp:43:8: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory] lagan20/src/faindex.cpp:42:25: note: Assuming allocation function fails lagan20/src/faindex.cpp:42:12: note: Assignment 'seq=(char*)malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/faindex.cpp:43:8: note: Null pointer dereference lagan20/src/faindex.cpp:54:8: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory] lagan20/src/faindex.cpp:53:25: note: Assuming allocation function fails lagan20/src/faindex.cpp:53:12: note: Assignment 'seq=(char*)malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/faindex.cpp:54:8: note: Null pointer dereference lagan20/src/faindex.cpp:9:6: style: struct member 'FaIndex::proto' is never used. [unusedStructMember] lagan20/src/diagmatrix.c:22:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:22:3: note: Null pointer dereference lagan20/src/diagmatrix.c:23:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:23:3: note: Null pointer dereference lagan20/src/diagmatrix.c:25:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:25:3: note: Null pointer dereference lagan20/src/diagmatrix.c:26:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:26:3: note: Null pointer dereference lagan20/src/diagmatrix.c:27:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:27:3: note: Null pointer dereference lagan20/src/diagmatrix.c:28:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:28:3: note: Null pointer dereference lagan20/src/diagmatrix.c:30:5: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:30:5: note: Null pointer dereference lagan20/src/diagmatrix.c:30:26: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:30:26: note: Null pointer dereference lagan20/src/diagmatrix.c:30:47: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:30:47: note: Null pointer dereference lagan20/src/diagmatrix.c:31:5: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:31:5: note: Null pointer dereference lagan20/src/diagmatrix.c:33:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:33:3: note: Null pointer dereference lagan20/src/diagmatrix.c:34:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:34:3: note: Null pointer dereference lagan20/src/diagmatrix.c:35:3: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:35:3: note: Null pointer dereference lagan20/src/diagmatrix.c:220:7: warning: If memory allocation fails, then there is a possible null pointer dereference: newptrs [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:218:30: note: Assuming allocation function fails lagan20/src/diagmatrix.c:218:15: note: Assignment 'newptrs=(char*)calloc((trgt->isneck[trgt->currdiag]+1)/2+1,sizeof(char))', assigned value is 0 lagan20/src/diagmatrix.c:220:7: note: Null pointer dereference lagan20/src/diagmatrix.c:197:34: style:inconclusive: Function 'DMsetElem' argument 2 names different: declaration 'elem' definition 'tbi'. [funcArgNamesDifferent] lagan20/src/diagmatrix.h:50:34: note: Function 'DMsetElem' argument 2 names different: declaration 'elem' definition 'tbi'. lagan20/src/diagmatrix.c:197:34: note: Function 'DMsetElem' argument 2 names different: declaration 'elem' definition 'tbi'. lagan20/src/diagmatrix.c:69:34: style: Parameter 'starts' can be declared as pointer to const [constParameterPointer] lagan20/src/diagmatrix.c:69:47: style: Parameter 'ends' can be declared as pointer to const [constParameterPointer] lagan20/src/diagmatrix.c:197:34: style: Parameter 'tbi' can be declared as pointer to const [constParameterPointer] lagan20/src/diagmatrix.c:73:18: style: Variable 'cond' is assigned a value that is never used. [unreadVariable] lagan20/src/diagmatrix.c:154:19: style: Unused variable: loc [unusedVariable] lagan20/src/diagmatrix.c:155:8: style: Unused variable: res [unusedVariable] lagan20/src/filebuffer.c:111:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/filebuffer.c:147:33: style: Condition 'currchar!='\t'' is always true [knownConditionTrueFalse] lagan20/src/filebuffer.c:18:13: error: Resource leak: data [resourceLeak] lagan20/src/filebuffer.c:100:5: error: Memory leak: res [memleak] lagan20/src/filebuffer.c:100:5: error: Memory leak: myseq [memleak] lagan20/src/filebuffer.c:69:7: error: Common realloc mistake: 'buffer' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/filebuffer.c:147:21: style: Same expression on both sides of '&&'. [duplicateExpression] lagan20/src/filebuffer.c:92:47: style:inconclusive: Function 'FileRead' argument 3 names different: declaration 'end' definition 'finish'. [funcArgNamesDifferent] lagan20/src/filebuffer.h:34:47: note: Function 'FileRead' argument 3 names different: declaration 'end' definition 'finish'. lagan20/src/filebuffer.c:92:47: note: Function 'FileRead' argument 3 names different: declaration 'end' definition 'finish'. lagan20/src/filebuffer.c:95:48: style: Variable 'resend' can be declared as pointer to const [constVariablePointer] lagan20/src/fchaos.c:233:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/fchaos.c:346:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/fchaos.c:775:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/global.c:42:3: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:42:3: note: Null pointer dereference lagan20/src/global.c:43:3: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:43:3: note: Null pointer dereference lagan20/src/global.c:44:3: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:44:3: note: Null pointer dereference lagan20/src/global.c:46:5: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:46:5: note: Null pointer dereference lagan20/src/global.c:46:17: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:46:17: note: Null pointer dereference lagan20/src/global.c:47:5: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:47:5: note: Null pointer dereference lagan20/src/global.c:48:5: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:48:5: note: Null pointer dereference lagan20/src/global.c:48:17: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:48:17: note: Null pointer dereference lagan20/src/global.c:51:5: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:51:5: note: Null pointer dereference lagan20/src/global.c:51:17: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:51:17: note: Null pointer dereference lagan20/src/global.c:52:5: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:52:5: note: Null pointer dereference lagan20/src/global.c:53:5: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:53:5: note: Null pointer dereference lagan20/src/global.c:53:17: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:53:17: note: Null pointer dereference lagan20/src/global.c:57:7: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:57:7: note: Null pointer dereference lagan20/src/global.c:57:21: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:57:21: note: Null pointer dereference lagan20/src/global.c:57:21: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:57:21: note: Null pointer dereference lagan20/src/global.c:58:7: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:58:7: note: Null pointer dereference lagan20/src/global.c:58:21: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:58:21: note: Null pointer dereference lagan20/src/global.c:58:21: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:58:21: note: Null pointer dereference lagan20/src/global.c:59:7: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:59:7: note: Null pointer dereference lagan20/src/global.c:59:21: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:59:21: note: Null pointer dereference lagan20/src/global.c:59:21: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:59:21: note: Null pointer dereference lagan20/src/global.c:59:21: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:59:21: note: Null pointer dereference lagan20/src/global.c:32:22: style:inconclusive: Function 'global' argument 7 names different: declaration 'gapstart' definition 'gapopen'. [funcArgNamesDifferent] lagan20/src/global.h:11:12: note: Function 'global' argument 7 names different: declaration 'gapstart' definition 'gapopen'. lagan20/src/global.c:32:22: note: Function 'global' argument 7 names different: declaration 'gapstart' definition 'gapopen'. lagan20/src/global.c:32:35: style:inconclusive: Function 'global' argument 8 names different: declaration 'gapcont' definition 'gapext'. [funcArgNamesDifferent] lagan20/src/global.h:11:26: note: Function 'global' argument 8 names different: declaration 'gapcont' definition 'gapext'. lagan20/src/global.c:32:35: note: Function 'global' argument 8 names different: declaration 'gapcont' definition 'gapext'. lagan20/src/global.c:31:21: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/global.c:31:55: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/global.c:129:22: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/global.c:129:56: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/global.c:130:26: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/global.c:34:31: style: Unused variable: score [unusedVariable] lagan20/src/ancseq.cpp:447:10: error: Array 'orgName[100]' accessed at index 100, which is out of bounds. [arrayIndexOutOfBounds] lagan20/src/ancseq.cpp:448:10: error: Array 'seqName[100]' accessed at index 100, which is out of bounds. [arrayIndexOutOfBounds] lagan20/src/ancseq.cpp:449:11: error: Array 'alignId1[100]' accessed at index 100, which is out of bounds. [arrayIndexOutOfBounds] lagan20/src/ancseq.cpp:450:11: error: Array 'alignId2[100]' accessed at index 100, which is out of bounds. [arrayIndexOutOfBounds] lagan20/src/ancseq.cpp:104:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/ancseq.cpp:455:4: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/ancseq.cpp:458:4: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/ancseq.cpp:461:4: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/ancseq.cpp:464:4: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/ancseq.cpp:169:8: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:168:25: note: Assuming allocation function fails lagan20/src/ancseq.cpp:168:12: note: Assignment 'buf=(char*)std::malloc(length*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:169:8: note: Null pointer dereference lagan20/src/ancseq.cpp:180:10: warning: If memory allocation fails, then there is a possible null pointer dereference: rev [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:178:26: note: Assuming allocation function fails lagan20/src/ancseq.cpp:178:13: note: Assignment 'rev=(char*)std::malloc(length*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:180:10: note: Null pointer dereference lagan20/src/ancseq.cpp:251:9: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:250:25: note: Assuming allocation function fails lagan20/src/ancseq.cpp:250:12: note: Assignment 'buf=(char*)std::malloc(size*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:251:9: note: Null pointer dereference lagan20/src/ancseq.cpp:253:10: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:250:25: note: Assuming allocation function fails lagan20/src/ancseq.cpp:250:12: note: Assignment 'buf=(char*)std::malloc(size*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:253:10: note: Null pointer dereference lagan20/src/ancseq.cpp:364:11: warning: If memory allocation fails, then there is a possible null pointer dereference: cons [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:363:22: note: Assuming allocation function fails lagan20/src/ancseq.cpp:363:9: note: Assignment 'cons=(char*)std::malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:364:11: note: Null pointer dereference lagan20/src/ancseq.cpp:168:12: style: C-style pointer casting [cstyleCast] lagan20/src/ancseq.cpp:178:13: style: C-style pointer casting [cstyleCast] lagan20/src/ancseq.cpp:250:12: style: C-style pointer casting [cstyleCast] lagan20/src/ancseq.cpp:363:9: style: C-style pointer casting [cstyleCast] lagan20/src/glocal/glocal.cpp:50:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEBUG [valueFlowBailoutIncompleteVar] lagan20/src/glocal/glocal.cpp:119:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq1 [valueFlowBailoutIncompleteVar] lagan20/src/glocal/glocal.cpp:187:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq1 [valueFlowBailoutIncompleteVar] lagan20/src/glocal/glocal.cpp:249:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEBUG [valueFlowBailoutIncompleteVar] lagan20/src/ancseq.cpp:703:13: style: Local variable 'i' shadows outer variable [shadowVariable] lagan20/src/ancseq.cpp:580:11: note: Shadowed declaration lagan20/src/ancseq.cpp:703:13: note: Shadow variable lagan20/src/ancseq.cpp:704:13: style: Local variable 'i' shadows outer variable [shadowVariable] lagan20/src/ancseq.cpp:580:11: note: Shadowed declaration lagan20/src/ancseq.cpp:704:13: note: Shadow variable lagan20/src/ancseq.cpp:49:33: performance: Function parameter 'header' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:217:29: performance: Function parameter 'genomeName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:217:47: performance: Function parameter 'protoNumber' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:217:66: performance: Function parameter 'genomePath' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:231:49: performance: Function parameter 'orgName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:231:77: performance: Function parameter 'seqName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:248:49: performance: Function parameter 'orgName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:248:77: performance: Function parameter 'seqName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:268:28: performance: Function parameter 'path' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:278:74: performance: Function parameter 'alignId' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:278:89: performance: Function parameter 'orgName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:355:23: performance: Function parameter 'alignId' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:374:85: performance: Function parameter 'alignId' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:374:100: performance: Function parameter 'orgName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:397:90: performance: Function parameter 'alignId' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:397:105: performance: Function parameter 'orgName' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:478:56: performance: Function parameter 'loc' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:482:43: performance: Function parameter 'chunk' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:491:33: performance: Function parameter 'outPath' should be passed by const reference. [passedByValue] lagan20/src/ancseq.cpp:40:20: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseq.cpp:126:30: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseq.cpp:136:28: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseq.cpp:148:33: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseq.cpp:157:31: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer] lagan20/src/ancseq.cpp:482:56: style: Parameter 'org' can be declared as const array [constParameter] lagan20/src/glocal/glocal.cpp:139:17: style: Variable 'current_score' is reassigned a value before the old one has been used. [redundantAssignment] lagan20/src/glocal/glocal.cpp:135:17: note: current_score is assigned lagan20/src/glocal/glocal.cpp:139:17: note: current_score is overwritten lagan20/src/glocal/glocal.cpp:146:17: style: Variable 'current_score' is reassigned a value before the old one has been used. [redundantAssignment] lagan20/src/glocal/glocal.cpp:139:17: note: current_score is assigned lagan20/src/glocal/glocal.cpp:146:17: note: current_score is overwritten lagan20/src/glocal/glocal.cpp:150:17: style: Variable 'current_score' is reassigned a value before the old one has been used. [redundantAssignment] lagan20/src/glocal/glocal.cpp:146:17: note: current_score is assigned lagan20/src/glocal/glocal.cpp:150:17: note: current_score is overwritten lagan20/src/glocal/glocal.cpp:153:17: style: Variable 'current_score' is reassigned a value before the old one has been used. [redundantAssignment] lagan20/src/glocal/glocal.cpp:150:17: note: current_score is assigned lagan20/src/glocal/glocal.cpp:153:17: note: current_score is overwritten lagan20/src/glocal/glocal.cpp:118:12: style: The scope of the variable 'owner' can be reduced. [variableScope] lagan20/src/glocal/glocal.cpp:120:8: style: The scope of the variable 'current_score' can be reduced. [variableScope] lagan20/src/ancseq.cpp:473:21: warning: Uninitialized variables: com.start, com.end [uninitvar] lagan20/src/ancseq.cpp:454:16: note: Assuming condition is false lagan20/src/ancseq.cpp:473:21: note: Uninitialized variables: com.start, com.end lagan20/src/ancseq.cpp:590:26: error: Uninitialized variable: chunk.strand [uninitvar] lagan20/src/ancseq.cpp:590:26: error: Uninitialized struct member: chunk.strand [uninitStructMember] lagan20/src/glocal/glocal.cpp:153:17: style: Variable 'current_score' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:380:12: style: Variable 'length' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:380:6: style: Variable 'length' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:403:12: style: Variable 'length' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:403:6: style: Variable 'length' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:518:11: style: Variable 'start' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:519:9: style: Variable 'end' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:540:10: style: Variable 'ancProto' is assigned a value that is never used. [unreadVariable] lagan20/src/ancseq.cpp:565:18: style: Variable 'orgIndex[org[2]]' is assigned a value that is never used. [unreadVariable] lagan20/src/glocal/io.cpp:94:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable POSITIVE [valueFlowBailoutIncompleteVar] lagan20/src/glocal/io.cpp:144:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable POSITIVE [valueFlowBailoutIncompleteVar] lagan20/src/glocal/io.cpp:195:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CUTOFF [valueFlowBailoutIncompleteVar] lagan20/src/glocal/io.cpp:214:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq1Start [valueFlowBailoutIncompleteVar] lagan20/src/glocal/io.cpp:236:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq1 [valueFlowBailoutIncompleteVar] lagan20/src/glocal/io.cpp:254:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq2Start [valueFlowBailoutIncompleteVar] lagan20/src/glocal/io.cpp:288:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nameIter [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:119:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:135:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RELPOSSHIFT [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:153:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FALSE [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:188:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:236:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:363:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:482:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:570:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEBUG [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:586:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEBUG [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:602:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEBUG [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:618:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEBUG [valueFlowBailoutIncompleteVar] lagan20/src/glocal/leftinfluence.cpp:630:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEBUG [valueFlowBailoutIncompleteVar] lagan20/src/glocal/io.cpp:13:19: warning: Identical inner 'return' condition is always true. [identicalInnerCondition] lagan20/src/glocal/io.cpp:12:14: note: outer condition: f1.seq1next=(struct gfc*)malloc(sizeof(struct gfc))', assigned value is 0 lagan20/src/fchaos.c:1107:24: note: Assignment '(*mygf)=(*mygf)->next', assigned value is 0 lagan20/src/fchaos.c:1108:8: note: Null pointer dereference lagan20/src/fchaos.c:1229:7: warning: Either the condition 'h1->last->next' is redundant or there is possible null pointer dereference: h2->first. [nullPointerRedundantCheck] lagan20/src/fchaos.c:1232:17: note: Assuming that condition 'h1->last->next' is not redundant lagan20/src/fchaos.c:1231:24: note: Assignment to 'h1->last->next=h2->first' lagan20/src/fchaos.c:1229:7: note: Null pointer dereference lagan20/src/fchaos.c:238:19: style: Parameter 'list1' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:238:31: style: Parameter 'list2' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:297:21: style: Parameter 'f' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:297:29: style: Parameter 's' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:392:17: style: Parameter 'arr' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:603:29: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:1003:41: style: Parameter 's1' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:1003:51: style: Parameter 's2' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:1020:59: style: Parameter 's1' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:1020:69: style: Parameter 's2' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:1054:46: style: Parameter 's1' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:1054:56: style: Parameter 's2' can be declared as pointer to const [constParameterPointer] lagan20/src/fchaos.c:353:32: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] lagan20/src/fchaos.c:830:12: warning: Uninitialized variables: currdbase.lets, currdbase.numlets, currdbase.numsiglets, currdbase.leftbound, currdbase.rightbound, currdbase.name, currdbase.rptr [uninitvar] lagan20/src/fchaos.c:830:12: note: Assuming condition is false lagan20/src/fchaos.c:863:17: note: Assignment 'currdbase=temp', assigned value is lagan20/src/fchaos.c:830:12: note: Uninitialized variables: currdbase.lets, currdbase.numlets, currdbase.numsiglets, currdbase.leftbound, currdbase.rightbound, currdbase.name, currdbase.rptr lagan20/src/fchaos.c:931:12: warning: Uninitialized variables: currdbase.lets, currdbase.numlets, currdbase.numsiglets, currdbase.leftbound, currdbase.rightbound, currdbase.name, currdbase.rptr [uninitvar] lagan20/src/fchaos.c:931:12: note: Assuming condition is false lagan20/src/fchaos.c:953:17: note: Assignment 'currdbase=temp', assigned value is lagan20/src/fchaos.c:931:12: note: Uninitialized variables: currdbase.lets, currdbase.numlets, currdbase.numsiglets, currdbase.leftbound, currdbase.rightbound, currdbase.name, currdbase.rptr lagan20/src/fchaos.c:302:24: style: Unused variable: temp [unusedVariable] lagan20/src/fchaos.c:401:12: style: Variable 'd1' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:401:18: style: Variable 'd2' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:401:7: style: Unused variable: i [unusedVariable] lagan20/src/fchaos.c:401:10: style: Variable 'd1' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:401:16: style: Variable 'd2' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:440:15: style: Variable 'doneset' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:440:7: style: Variable 'doneset' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:542:18: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:543:19: style: Variable 'bestqueryloc' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:543:36: style: Variable 'bestdbaseloc' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:542:9: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:543:7: style: Variable 'bestqueryloc' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:543:24: style: Variable 'bestdbaseloc' is assigned a value that is never used. [unreadVariable] lagan20/src/fchaos.c:885:7: style: Unused variable: i [unusedVariable] lagan20/src/fchaos.c:970:7: style: Unused variable: temp [unusedVariable] lagan20/src/fchaos.c:1147:9: style: Variable 'j' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:81:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:139:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:147:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:170:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:247:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:259:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:296:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scoreSoFar [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:492:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:562:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:580:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:665:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:697:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:714:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:869:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/mlagan.c:951:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/order.c:63:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/order.c:267:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/order.c:329:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/order.c:438:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/order.c:628:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:282:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:424:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:544:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:673:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:841:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:921:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:1133:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:1469:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:1528:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:1556:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/order.c:782:6: style: Condition 'hasst' is always false [knownConditionTrueFalse] lagan20/src/order.c:774:13: note: Assignment 'hasst=0', assigned value is 0 lagan20/src/order.c:782:6: note: Condition 'hasst' is always false lagan20/src/order.c:814:6: style: Condition 'hasst' is always false [knownConditionTrueFalse] lagan20/src/order.c:806:13: note: Assignment 'hasst=0', assigned value is 0 lagan20/src/order.c:814:6: note: Condition 'hasst' is always false lagan20/src/order.c:60:5: error: Memory leak: res [memleak] lagan20/src/order.c:60:5: error: Memory leak: myseq [memleak] lagan20/src/order.c:79:2: error: Common realloc mistake: 'res' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/order.c:544:6: error: Common realloc mistake: 'almt' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/order.c:237:10: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/order.c:233:23: note: Assuming allocation function fails lagan20/src/order.c:233:10: note: Assignment 'tt=(struct hll*)malloc(sizeof(struct hll))', assigned value is 0 lagan20/src/order.c:237:10: note: Null pointer dereference lagan20/src/order.c:237:38: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/order.c:233:23: note: Assuming allocation function fails lagan20/src/order.c:233:10: note: Assignment 'tt=(struct hll*)malloc(sizeof(struct hll))', assigned value is 0 lagan20/src/order.c:237:38: note: Null pointer dereference lagan20/src/order.c:238:3: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/order.c:233:23: note: Assuming allocation function fails lagan20/src/order.c:233:10: note: Assignment 'tt=(struct hll*)malloc(sizeof(struct hll))', assigned value is 0 lagan20/src/order.c:238:3: note: Null pointer dereference lagan20/src/order.c:238:31: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/order.c:233:23: note: Assuming allocation function fails lagan20/src/order.c:233:10: note: Assignment 'tt=(struct hll*)malloc(sizeof(struct hll))', assigned value is 0 lagan20/src/order.c:238:31: note: Null pointer dereference lagan20/src/order.c:493:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/order.c:487:32: note: Assuming allocation function fails lagan20/src/order.c:487:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/order.c:493:3: note: Null pointer dereference lagan20/src/order.c:494:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/order.c:487:32: note: Assuming allocation function fails lagan20/src/order.c:487:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/order.c:494:3: note: Null pointer dereference lagan20/src/order.c:495:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/order.c:487:32: note: Assuming allocation function fails lagan20/src/order.c:487:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/order.c:495:3: note: Null pointer dereference lagan20/src/order.c:496:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/order.c:487:32: note: Assuming allocation function fails lagan20/src/order.c:487:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/order.c:496:3: note: Null pointer dereference lagan20/src/order.c:126:29: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:485:35: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:485:47: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:560:9: style: Variable 'first' can be declared as pointer to const [constVariablePointer] lagan20/src/order.c:561:6: style: Variable 'second' can be declared as pointer to const [constVariablePointer] lagan20/src/order.c:586:10: style: Variable 'n' can be declared as pointer to const [constVariablePointer] lagan20/src/order.c:707:25: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:707:37: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:707:50: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:727:26: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:727:38: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:727:51: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:771:25: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:771:37: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:771:50: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:771:65: style: Parameter 'n1' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:771:75: style: Parameter 'n2' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:803:26: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:803:38: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:803:51: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:803:66: style: Parameter 'n1' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:803:76: style: Parameter 'n2' can be declared as pointer to const [constParameterPointer] lagan20/src/order.c:71:32: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] lagan20/src/order.c:274:7: style: Unused variable: incr [unusedVariable] lagan20/src/order.c:486:7: style: Unused variable: temp [unusedVariable] lagan20/src/order.c:560:15: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:561:13: style: Variable 'second' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:560:9: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:561:6: style: Variable 'second' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:586:12: style: Variable 'n' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:586:10: style: Variable 'n' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:619:10: style: Variable 'isneck' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:662:10: style: Variable 's1' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:663:10: style: Variable 's2' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:664:10: style: Variable 's3' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:773:9: style: Variable 'nm' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:773:32: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:773:7: style: Variable 'nm' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:773:27: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:805:9: style: Variable 'nm' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:805:32: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:805:7: style: Variable 'nm' is assigned a value that is never used. [unreadVariable] lagan20/src/order.c:805:27: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:564:2: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn] lagan20/src/mlagan.c:550:24: style: Condition 'treestr[i]==')'' is always false [knownConditionTrueFalse] lagan20/src/mlagan.c:93:9: warning: fprintf format string requires 1 parameter but 2 are given. [wrongPrintfScanfArgNum] lagan20/src/mlagan.c:126:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/mlagan.c:606:5: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/mlagan.c:78:5: error: Memory leak: res [memleak] lagan20/src/mlagan.c:78:5: error: Memory leak: myseq [memleak] lagan20/src/mlagan.c:963:53: error: Memory leak: seqs [memleak] lagan20/src/mlagan.c:98:9: error: Common realloc mistake: 'res' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/mlagan.c:76:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/mlagan.c:70:29: note: Assuming allocation function fails lagan20/src/mlagan.c:70:15: note: Assignment 'res=(char*)malloc(sizeof(char)*2)', assigned value is 0 lagan20/src/mlagan.c:76:3: note: Null pointer dereference lagan20/src/mlagan.c:126:21: warning: If memory allocation fails, then there is a possible null pointer dereference: first_word [nullPointerOutOfMemory] lagan20/src/mlagan.c:125:30: note: Assuming allocation function fails lagan20/src/mlagan.c:125:16: note: Assignment 'first_word=(char*)malloc((len+1)*sizeof(char))', assigned value is 0 lagan20/src/mlagan.c:126:21: note: Null pointer dereference lagan20/src/mlagan.c:127:23: warning: If memory allocation fails, then there is a possible null pointer dereference: first_word [nullPointerOutOfMemory] lagan20/src/mlagan.c:125:30: note: Assuming allocation function fails lagan20/src/mlagan.c:125:16: note: Assignment 'first_word=(char*)malloc((len+1)*sizeof(char))', assigned value is 0 lagan20/src/mlagan.c:127:23: note: Null pointer dereference lagan20/src/mlagan.c:182:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/mlagan.c:179:23: note: Assuming allocation function fails lagan20/src/mlagan.c:179:10: note: Assignment 'tt=(struct HitLocationList*)malloc(sizeof(struct HitLocationList))', assigned value is 0 lagan20/src/mlagan.c:182:5: note: Null pointer dereference lagan20/src/mlagan.c:278:9: warning: If memory allocation fails, then there is a possible null pointer dereference: array [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:341:24: note: Calling function 'findBestChain', 1st argument 'myptrs' value is 0 lagan20/src/mlagan.c:278:9: note: Null pointer dereference lagan20/src/mlagan.c:332:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:332:5: note: Null pointer dereference lagan20/src/mlagan.c:333:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:333:5: note: Null pointer dereference lagan20/src/mlagan.c:334:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:334:5: note: Null pointer dereference lagan20/src/mlagan.c:335:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:335:5: note: Null pointer dereference lagan20/src/mlagan.c:336:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:336:5: note: Null pointer dereference lagan20/src/mlagan.c:337:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:337:5: note: Null pointer dereference lagan20/src/mlagan.c:340:9: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/mlagan.c:330:27: note: Assuming allocation function fails lagan20/src/mlagan.c:330:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/mlagan.c:340:9: note: Null pointer dereference lagan20/src/mlagan.c:108:16: style: The comparison 'seqstart > 0' is always false. [knownConditionTrueFalse] lagan20/src/mlagan.c:68:16: note: 'seqstart' is assigned value '0' here. lagan20/src/mlagan.c:108:16: note: The comparison 'seqstart > 0' is always false. lagan20/src/mlagan.c:110:15: style: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. [duplicateExpression] lagan20/src/mlagan.c:69:14: note: 'seqend' is assigned value '0' here. lagan20/src/mlagan.c:68:16: note: 'seqstart' is assigned value '0' here. lagan20/src/mlagan.c:110:15: note: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. lagan20/src/mlagan.c:111:21: style: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. [duplicateExpression] lagan20/src/mlagan.c:69:14: note: 'seqend' is assigned value '0' here. lagan20/src/mlagan.c:68:16: note: 'seqstart' is assigned value '0' here. lagan20/src/mlagan.c:111:21: note: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. lagan20/src/mlagan.c:120:23: style: Parameter 'str' can be declared as pointer to const [constParameterPointer] lagan20/src/mlagan.c:120:34: style: Parameter 'word' can be declared as pointer to const [constParameterPointer] lagan20/src/mlagan.c:130:47: style: Parameter 'name' can be declared as pointer to const [constParameterPointer] lagan20/src/mlagan.c:159:29: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer] lagan20/src/mlagan.c:161:29: style: Variable 'first' can be declared as pointer to const [constVariablePointer] lagan20/src/mlagan.c:208:9: style: Variable 'name1' can be declared as pointer to const [constVariablePointer] lagan20/src/mlagan.c:208:17: style: Variable 'name2' can be declared as pointer to const [constVariablePointer] lagan20/src/mlagan.c:209:9: style: Variable 'endpnt' can be declared as pointer to const [constVariablePointer] lagan20/src/mlagan.c:255:40: style: Parameter 'myseq' can be declared as pointer to const [constParameterPointer] lagan20/src/mlagan.c:377:52: style: Parameter 'index' can be declared as pointer to const [constParameterPointer] lagan20/src/mlagan.c:593:25: style: Parameter 'simalign' can be declared as const array [constParameter] lagan20/src/mlagan.c:89:32: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] lagan20/src/mlagan.c:589:10: warning: Uninitialized variables: stack.num, stack.index, stack.score, stack.algnlen, stack.numseq, stack.algn, stack.dirty, stack.nextalign [uninitvar] lagan20/src/mlagan.c:572:12: note: Assuming condition is false lagan20/src/mlagan.c:589:10: note: Uninitialized variables: stack.num, stack.index, stack.score, stack.algnlen, stack.numseq, stack.algn, stack.dirty, stack.nextalign lagan20/src/mlagan.c:38:10: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:38:7: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:161:23: style: Variable 'tt' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:161:35: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:161:29: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:213:13: style: Variable 'flip' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:211:10: style: Unused variable: temp [unusedVariable] lagan20/src/mlagan.c:213:8: style: Variable 'flip' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:310:19: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:307:7: style: Unused variable: len [unusedVariable] lagan20/src/mlagan.c:309:15: style: Unused variable: t2 [unusedVariable] lagan20/src/mlagan.c:309:20: style: Unused variable: t3 [unusedVariable] lagan20/src/mlagan.c:310:7: style: Unused variable: i [unusedVariable] lagan20/src/mlagan.c:310:10: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:483:12: style: Unused variable: oldscore [unusedVariable] lagan20/src/mlagan.c:485:10: style: Unused variable: readd [unusedVariable] lagan20/src/mlagan.c:528:16: style: Unused variable: j [unusedVariable] lagan20/src/mlagan.c:673:13: style: Variable 'sum' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:673:25: style: Variable 'length' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:674:15: style: Variable 'score' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:674:26: style: Variable 'count' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:684:25: style: Variable 'score' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:689:8: style: Variable 'score' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:941:16: style: Variable 'j' is assigned a value that is never used. [unreadVariable] lagan20/src/mlagan.c:939:14: style: Unused variable: seqfile [unusedVariable] lagan20/src/mlagan.c:941:21: style: Unused variable: x [unusedVariable] lagan20/src/mlagan.c:941:24: style: Unused variable: y [unusedVariable] lagan20/src/mlagan.c:942:8: style: Unused variable: command [unusedVariable] lagan20/src/skiplist.c:36:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:81:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:139:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:215:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:232:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:255:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:332:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:344:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:381:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scoreSoFar [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:560:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:568:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:594:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:664:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:687:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:703:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:716:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:884:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:969:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/skiplist.c:12:3: warning: %x in format string (no. 2) requires 'unsigned int' but the argument type is 'void *'. [invalidPrintfArgType_uint] lagan20/src/skiplist.c:184:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/skiplist.c:183:27: note: Assuming allocation function fails lagan20/src/skiplist.c:183:14: note: Assignment 'res=(struct sle*)malloc(sizeof(struct sle))', assigned value is 0 lagan20/src/skiplist.c:184:3: note: Null pointer dereference lagan20/src/skiplist.c:185:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/skiplist.c:183:27: note: Assuming allocation function fails lagan20/src/skiplist.c:183:14: note: Assignment 'res=(struct sle*)malloc(sizeof(struct sle))', assigned value is 0 lagan20/src/skiplist.c:185:3: note: Null pointer dereference lagan20/src/skiplist.c:186:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/skiplist.c:183:27: note: Assuming allocation function fails lagan20/src/skiplist.c:183:14: note: Assignment 'res=(struct sle*)malloc(sizeof(struct sle))', assigned value is 0 lagan20/src/skiplist.c:186:3: note: Null pointer dereference lagan20/src/skiplist.c:187:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/skiplist.c:183:27: note: Assuming allocation function fails lagan20/src/skiplist.c:183:14: note: Assignment 'res=(struct sle*)malloc(sizeof(struct sle))', assigned value is 0 lagan20/src/skiplist.c:187:3: note: Null pointer dereference lagan20/src/skiplist.c:188:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/skiplist.c:183:27: note: Assuming allocation function fails lagan20/src/skiplist.c:183:14: note: Assignment 'res=(struct sle*)malloc(sizeof(struct sle))', assigned value is 0 lagan20/src/skiplist.c:188:3: note: Null pointer dereference lagan20/src/skiplist.c:190:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/skiplist.c:183:27: note: Assuming allocation function fails lagan20/src/skiplist.c:183:14: note: Assignment 'res=(struct sle*)malloc(sizeof(struct sle))', assigned value is 0 lagan20/src/skiplist.c:190:5: note: Null pointer dereference lagan20/src/skiplist.c:191:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/skiplist.c:183:27: note: Assuming allocation function fails lagan20/src/skiplist.c:183:14: note: Assignment 'res=(struct sle*)malloc(sizeof(struct sle))', assigned value is 0 lagan20/src/skiplist.c:191:5: note: Null pointer dereference lagan20/src/skiplist.c:11:20: style: Parameter 'tbp' can be declared as pointer to const [constParameterPointer] lagan20/src/skiplist.c:105:22: style: Parameter 'trgt' can be declared as pointer to const [constParameterPointer] lagan20/src/skiplist.c:33:7: style: Unused variable: i [unusedVariable] lagan20/src/skiplist.c:100:37: style: Unused variable: tbe [unusedVariable] lagan20/src/sortlist.c:41:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg] lagan20/src/sortlist.c:34:0: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn] lagan20/src/sortlist.c:40:7: style: Variable 'mid' is reassigned a value before the old one has been used. [redundantAssignment] lagan20/src/sortlist.c:37:7: note: mid is assigned lagan20/src/sortlist.c:40:7: note: mid is overwritten lagan20/src/sortlist.c:41:10: style: Variable 'mylist' is assigned a value that is never used. [unreadVariable] lagan20/src/thrtrie.c:217:5: error: Common realloc mistake: 'jobqueue' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/thrtrie.c:235:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/thrtrie.c:234:25: note: Assuming allocation function fails lagan20/src/thrtrie.c:234:9: note: Assignment 'res=(struct LList*)malloc(sizeof(struct LList))', assigned value is 0 lagan20/src/thrtrie.c:235:3: note: Null pointer dereference lagan20/src/thrtrie.c:236:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/thrtrie.c:234:25: note: Assuming allocation function fails lagan20/src/thrtrie.c:234:9: note: Assignment 'res=(struct LList*)malloc(sizeof(struct LList))', assigned value is 0 lagan20/src/thrtrie.c:236:3: note: Null pointer dereference lagan20/src/thrtrie.c:239:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/thrtrie.c:234:25: note: Assuming allocation function fails lagan20/src/thrtrie.c:234:9: note: Assignment 'res=(struct LList*)malloc(sizeof(struct LList))', assigned value is 0 lagan20/src/thrtrie.c:239:5: note: Null pointer dereference lagan20/src/thrtrie.c:240:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/thrtrie.c:234:25: note: Assuming allocation function fails lagan20/src/thrtrie.c:234:9: note: Assignment 'res=(struct LList*)malloc(sizeof(struct LList))', assigned value is 0 lagan20/src/thrtrie.c:240:3: note: Null pointer dereference lagan20/src/thrtrie.c:62:23: style:inconclusive: Function 'freeTrie' argument 1 names different: declaration 'root' definition 'trgt'. [funcArgNamesDifferent] lagan20/src/thrtrie.h:56:23: note: Function 'freeTrie' argument 1 names different: declaration 'root' definition 'trgt'. lagan20/src/thrtrie.c:62:23: note: Function 'freeTrie' argument 1 names different: declaration 'root' definition 'trgt'. lagan20/src/thrtrie.c:122:23: style:inconclusive: Function 'insertWord' argument 1 names different: declaration 'root' definition 'currnode'. [funcArgNamesDifferent] lagan20/src/thrtrie.h:58:23: note: Function 'insertWord' argument 1 names different: declaration 'root' definition 'currnode'. lagan20/src/thrtrie.c:122:23: note: Function 'insertWord' argument 1 names different: declaration 'root' definition 'currnode'. lagan20/src/thrtrie.c:172:38: style:inconclusive: Function 'insertString' argument 2 names different: declaration 'tbi' definition 'word'. [funcArgNamesDifferent] lagan20/src/thrtrie.h:66:38: note: Function 'insertString' argument 2 names different: declaration 'tbi' definition 'word'. lagan20/src/thrtrie.c:172:38: note: Function 'insertString' argument 2 names different: declaration 'tbi' definition 'word'. lagan20/src/thrtrie.c:244:29: style:inconclusive: Function 'getNextWords' argument 1 names different: declaration 'root' definition 'currnode'. [funcArgNamesDifferent] lagan20/src/thrtrie.h:65:28: note: Function 'getNextWords' argument 1 names different: declaration 'root' definition 'currnode'. lagan20/src/thrtrie.c:244:29: note: Function 'getNextWords' argument 1 names different: declaration 'root' definition 'currnode'. lagan20/src/thrtrie.c:19:22: style: Parameter 'alpha' can be declared as pointer to const [constParameterPointer] lagan20/src/thrtrie.c:62:23: style: Parameter 'trgt' can be declared as pointer to const [constParameterPointer] lagan20/src/thrtrie.c:230:34: style: Parameter 'word' can be declared as pointer to const [constParameterPointer] lagan20/src/thrtrie.c:174:10: style: Unused variable: j [unusedVariable] lagan20/src/thrtrie.c:251:14: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/translate.c:22:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/translate.c:40:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/translate.c:8:23: style: Parameter 'dnaword' can be declared as pointer to const [constParameterPointer] lagan20/src/translate.c:10:9: style: Variable 'table' can be declared as pointer to const [constVariablePointer] lagan20/src/translate.c:9:10: style: Unused variable: j [unusedVariable] lagan20/src/multial.c:83:0: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn] lagan20/src/multial.c:1039:10: style: Condition 'j' is always true [knownConditionTrueFalse] lagan20/src/multial.c:1032:9: note: Assuming that condition 'j<=1' is not redundant lagan20/src/multial.c:1039:10: note: Condition 'j' is always true lagan20/src/multial.c:270:5: error: Common realloc mistake: 'freed' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/multial.c:271:5: error: Common realloc mistake: 'freedptr' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/multial.c:339:7: error: Common realloc mistake: 'almt' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/multial.c:995:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:994:31: note: Assuming allocation function fails lagan20/src/multial.c:994:16: note: Assignment 'res=(struct align_res*)malloc(sizeof(struct align_res))', assigned value is 0 lagan20/src/multial.c:995:3: note: Null pointer dereference lagan20/src/multial.c:996:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:994:31: note: Assuming allocation function fails lagan20/src/multial.c:994:16: note: Assignment 'res=(struct align_res*)malloc(sizeof(struct align_res))', assigned value is 0 lagan20/src/multial.c:996:3: note: Null pointer dereference lagan20/src/multial.c:998:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:994:31: note: Assuming allocation function fails lagan20/src/multial.c:994:16: note: Assignment 'res=(struct align_res*)malloc(sizeof(struct align_res))', assigned value is 0 lagan20/src/multial.c:998:5: note: Null pointer dereference lagan20/src/multial.c:1000:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:994:31: note: Assuming allocation function fails lagan20/src/multial.c:994:16: note: Assignment 'res=(struct align_res*)malloc(sizeof(struct align_res))', assigned value is 0 lagan20/src/multial.c:1000:5: note: Null pointer dereference lagan20/src/multial.c:1002:6: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:994:31: note: Assuming allocation function fails lagan20/src/multial.c:994:16: note: Assignment 'res=(struct align_res*)malloc(sizeof(struct align_res))', assigned value is 0 lagan20/src/multial.c:1002:6: note: Null pointer dereference lagan20/src/multial.c:1004:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:994:31: note: Assuming allocation function fails lagan20/src/multial.c:994:16: note: Assignment 'res=(struct align_res*)malloc(sizeof(struct align_res))', assigned value is 0 lagan20/src/multial.c:1004:5: note: Null pointer dereference lagan20/src/multial.c:1356:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:1353:21: note: Assuming allocation function fails lagan20/src/multial.c:1353:21: note: Assignment 'res=malloc(sizeof(struct HitLocationList))', assigned value is 0 lagan20/src/multial.c:1356:3: note: Null pointer dereference lagan20/src/multial.c:1357:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:1353:21: note: Assuming allocation function fails lagan20/src/multial.c:1353:21: note: Assignment 'res=malloc(sizeof(struct HitLocationList))', assigned value is 0 lagan20/src/multial.c:1357:3: note: Null pointer dereference lagan20/src/multial.c:1359:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:1353:21: note: Assuming allocation function fails lagan20/src/multial.c:1353:21: note: Assignment 'res=malloc(sizeof(struct HitLocationList))', assigned value is 0 lagan20/src/multial.c:1359:3: note: Null pointer dereference lagan20/src/multial.c:1360:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:1353:21: note: Assuming allocation function fails lagan20/src/multial.c:1353:21: note: Assignment 'res=malloc(sizeof(struct HitLocationList))', assigned value is 0 lagan20/src/multial.c:1360:3: note: Null pointer dereference lagan20/src/multial.c:1361:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/multial.c:1353:21: note: Assuming allocation function fails lagan20/src/multial.c:1353:21: note: Assignment 'res=malloc(sizeof(struct HitLocationList))', assigned value is 0 lagan20/src/multial.c:1361:3: note: Null pointer dereference lagan20/src/multial.c:1232:2: style: Variable 'temp' is assigned an expression that holds the same value. [redundantAssignment] lagan20/src/multial.c:1228:13: note: anchs is assigned 'temp' here. lagan20/src/multial.c:1232:2: note: Variable 'temp' is assigned an expression that holds the same value. lagan20/src/multial.c:1080:19: style:inconclusive: Function 'swapHLL' argument 1 names different: declaration 'arg' definition 'h1'. [funcArgNamesDifferent] lagan20/src/multial.h:69:19: note: Function 'swapHLL' argument 1 names different: declaration 'arg' definition 'h1'. lagan20/src/multial.c:1080:19: note: Function 'swapHLL' argument 1 names different: declaration 'arg' definition 'h1'. lagan20/src/multial.c:1464:26: style:inconclusive: Function 'printTextAlign' argument 1 names different: declaration 'seq1' definition 'outfile'. [funcArgNamesDifferent] lagan20/src/order.h:20:26: note: Function 'printTextAlign' argument 1 names different: declaration 'seq1' definition 'outfile'. lagan20/src/multial.c:1464:26: note: Function 'printTextAlign' argument 1 names different: declaration 'seq1' definition 'outfile'. lagan20/src/multial.c:1464:42: style:inconclusive: Function 'printTextAlign' argument 2 names different: declaration 'seq2' definition 'myalign'. [funcArgNamesDifferent] lagan20/src/order.h:20:38: note: Function 'printTextAlign' argument 2 names different: declaration 'seq2' definition 'myalign'. lagan20/src/multial.c:1464:42: note: Function 'printTextAlign' argument 2 names different: declaration 'seq2' definition 'myalign'. lagan20/src/multial.c:1594:24: style:inconclusive: Function 'freeSequence' argument 1 names different: declaration 'mySequence' definition 'mySeq'. [funcArgNamesDifferent] lagan20/src/multial.h:80:24: note: Function 'freeSequence' argument 1 names different: declaration 'mySequence' definition 'mySeq'. lagan20/src/multial.c:1594:24: note: Function 'freeSequence' argument 1 names different: declaration 'mySequence' definition 'mySeq'. lagan20/src/multial.c:1602:23: style:inconclusive: Function 'freeAlign' argument 1 names different: declaration 't' definition 'myAlign'. [funcArgNamesDifferent] lagan20/src/order.h:18:23: note: Function 'freeAlign' argument 1 names different: declaration 't' definition 'myAlign'. lagan20/src/multial.c:1602:23: note: Function 'freeAlign' argument 1 names different: declaration 't' definition 'myAlign'. lagan20/src/multial.c:804:7: style: Local variable 'gapend' shadows outer variable [shadowVariable] lagan20/src/multial.h:94:12: note: Shadowed declaration lagan20/src/multial.c:804:7: note: Shadow variable lagan20/src/multial.c:154:25: style: Parameter 'ali' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:357:9: style: Variable 'first' can be declared as pointer to const [constVariablePointer] lagan20/src/multial.c:358:6: style: Variable 'second' can be declared as pointer to const [constVariablePointer] lagan20/src/multial.c:381:10: style: Variable 'n' can be declared as pointer to const [constVariablePointer] lagan20/src/multial.c:448:29: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:496:64: style: Parameter 'substmatrix' can be declared as const array [constParameter] lagan20/src/multial.c:503:9: style: Variable 'lets' can be declared as pointer to const [constVariablePointer] lagan20/src/multial.c:549:30: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:549:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:562:29: style: Parameter 'other' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:569:28: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:569:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:574:28: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:574:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:580:28: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:580:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:585:27: style: Parameter 'ali' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:585:48: style: Parameter 'other' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:585:68: style: Parameter 'sopp' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:593:46: style: Parameter 'other' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:593:66: style: Parameter 'sopp' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:593:78: style: Parameter 'desc' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:787:32: style: Parameter 'ali1' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:787:45: style: Parameter 'ali2' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1059:42: style: Parameter 'name' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1062:8: style: Variable 'removed' can be declared as pointer to const [constVariablePointer] lagan20/src/multial.c:1070:22: style: Parameter 'ali' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1070:32: style: Parameter 'trgt' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1384:28: style: Parameter 'a' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1394:22: style: Parameter 'myres' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1464:42: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1523:43: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:1551:42: style: Parameter 'myalign' can be declared as pointer to const [constParameterPointer] lagan20/src/multial.c:103:26: style: Variable 'isfrst' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:99:20: style: Unused variable: oldscore [unusedVariable] lagan20/src/multial.c:99:30: style: Unused variable: peakscore [unusedVariable] lagan20/src/multial.c:103:19: style: Variable 'isfrst' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:104:9: style: Unused variable: peakfrac [unusedVariable] lagan20/src/multial.c:187:14: style: Unused variable: cbc [unusedVariable] lagan20/src/multial.c:187:19: style: Unused variable: brcount [unusedVariable] lagan20/src/multial.c:188:23: style: Unused variable: tgs [unusedVariable] lagan20/src/multial.c:188:28: style: Unused variable: tgc [unusedVariable] lagan20/src/multial.c:247:7: style: Unused variable: temp [unusedVariable] lagan20/src/multial.c:357:15: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:358:13: style: Variable 'second' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:357:9: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:358:6: style: Variable 'second' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:381:12: style: Variable 'n' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:381:10: style: Variable 'n' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:594:15: style: Unused variable: pen [unusedVariable] lagan20/src/multial.c:594:25: style: Unused variable: i [unusedVariable] lagan20/src/multial.c:615:7: style: Unused variable: incr [unusedVariable] lagan20/src/multial.c:802:17: style: Variable 'gapstartN' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:802:32: style: Variable 'gapstartO' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:808:15: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:811:28: style: Variable 'oldneck' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:817:10: style: Variable 'isneck' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:891:15: style: Variable 'oldneck' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:804:7: style: Unused variable: gapend [unusedVariable] lagan20/src/multial.c:805:7: style: Unused variable: tt [unusedVariable] lagan20/src/multial.c:805:11: style: Unused variable: prevgap [unusedVariable] lagan20/src/multial.c:807:14: style: Unused variable: b [unusedVariable] lagan20/src/multial.c:808:8: style: Unused variable: rh [unusedVariable] lagan20/src/multial.c:1065:11: style: Variable 'removed' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1073:8: style: Unused variable: removed [unusedVariable] lagan20/src/multial.c:1104:43: style: Unused variable: olen [unusedVariable] lagan20/src/multial.c:1352:7: style: Unused variable: i [unusedVariable] lagan20/src/multial.c:1352:10: style: Unused variable: j [unusedVariable] lagan20/src/multial.c:1368:10: style: Unused variable: j [unusedVariable] lagan20/src/multial.c:1408:7: style: Unused variable: i [unusedVariable] lagan20/src/multial.c:1408:10: style: Unused variable: j [unusedVariable] lagan20/src/multial.c:1465:9: style: Variable 's1' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1465:15: style: Variable 's2' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1466:12: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1465:7: style: Variable 's1' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1465:13: style: Variable 's2' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1466:7: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1524:9: style: Variable 's1' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/Sequence.h:202:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] lagan20/src/utils/Sequence.h:217:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:1524:15: style: Variable 's2' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/Output.h:9:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] lagan20/src/utils/Glue.cpp:34:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/Glue.cpp:172:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] lagan20/src/utils/Glue.cpp:185:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] lagan20/src/utils/Glue.cpp:225:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] lagan20/src/utils/Glue.cpp:357:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] lagan20/src/multial.c:1525:12: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1524:7: style: Variable 's1' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1524:13: style: Variable 's2' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1525:7: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1552:9: style: Variable 's1' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1552:15: style: Variable 's2' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1553:12: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1552:7: style: Variable 's1' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1552:13: style: Variable 's2' is assigned a value that is never used. [unreadVariable] lagan20/src/multial.c:1553:7: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/bin2bl.c:68:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] lagan20/src/utils/bin2bl.c:183:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/Sequence.h:157:5: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg] lagan20/src/utils/Sequence.h:71:3: warning: Member variable 'Sequence::id' is not initialized in the constructor. [uninitMemberVar] lagan20/src/utils/Sequence.h:80:3: style: Class 'Sequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] lagan20/src/utils/SafeVector.h:22:3: style: Class 'SafeVector < char >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] lagan20/src/utils/SafeVector.h:22:3: style: Class 'SafeVector < Sequence >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] lagan20/src/utils/SafeVector.h:22:3: style: Class 'SafeVector < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] lagan20/src/utils/SafeVector.h:22:3: style: Class 'SafeVector < SafeVector < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] lagan20/src/utils/SafeVector.h:22:3: style: Class 'SafeVector < SafeVector < SafeVector < int > > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] lagan20/src/utils/Sequence.h:168:16: performance: Function 'getComment()' should return member 'comment' by const reference. [returnByReference] lagan20/src/utils/Sequence.h:39:19: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/utils/Glue.cpp:293:7: style: The scope of the variable 'num1' can be reduced. [variableScope] lagan20/src/utils/Glue.cpp:322:7: style: The scope of the variable 'num1' can be reduced. [variableScope] lagan20/src/utils/Glue.cpp:375:19: style: The scope of the variable 'end1' can be reduced. [variableScope] lagan20/src/utils/Glue.cpp:66:12: style: Local variable 'i' shadows outer variable [shadowVariable] lagan20/src/utils/Glue.cpp:64:7: note: Shadowed declaration lagan20/src/utils/Glue.cpp:66:12: note: Shadow variable lagan20/src/utils/Glue.cpp:67:14: style: Local variable 'j' shadows outer variable [shadowVariable] lagan20/src/utils/Glue.cpp:64:10: note: Shadowed declaration lagan20/src/utils/Glue.cpp:67:14: note: Shadow variable lagan20/src/utils/Glue.cpp:176:7: style: Local variable 'score' shadows outer variable [shadowVariable] lagan20/src/utils/Glue.cpp:22:10: note: Shadowed declaration lagan20/src/utils/Glue.cpp:176:7: note: Shadow variable lagan20/src/utils/Glue.cpp:200:29: style: Local variable 'score' shadows outer variable [shadowVariable] lagan20/src/utils/Glue.cpp:22:10: note: Shadowed declaration lagan20/src/utils/Glue.cpp:200:29: note: Shadow variable lagan20/src/utils/Glue.cpp:264:7: style: Local variable 'score' shadows outer variable [shadowVariable] lagan20/src/utils/Glue.cpp:22:10: note: Shadowed declaration lagan20/src/utils/Glue.cpp:264:7: note: Shadow variable lagan20/src/utils/Output.h:5:65: performance: Function parameter 'comment' should be passed by const reference. [passedByValue] lagan20/src/utils/MultiSequence.h:36:17: style: Variable 'seq' can be declared as reference to const [constVariableReference] lagan20/src/utils/Glue.cpp:238:27: style: Parameter 'data1a' can be declared as reference to const [constParameterReference] lagan20/src/utils/Glue.cpp:238:53: style: Parameter 'data2a' can be declared as reference to const [constParameterReference] lagan20/src/utils/Glue.cpp:26:29: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/Glue.cpp:30:9: style: Variable 'lagan_dir' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/Glue.cpp:63:9: style: Variable 'alpha' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/Sequence.h:157:13: style: Variable 'comment' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/Glue.cpp:200:23: style: Variable 'end' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/Glue.cpp:220:14: style: Variable 'end' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/Glue.cpp:375:24: style: Variable 'end1' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:666:2: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn] lagan20/src/utils/bin2mf.c:29:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] lagan20/src/utils/bin2mf.c:65:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/bin2bl.c:14:9: style: Variable 'slash' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/bin2bl.c:27:8: style: Variable 'bases' can be declared as const array [constVariable] lagan20/src/utils/bin2bl.c:34:8: style: Variable 'font_start' can be declared as const array [constVariable] lagan20/src/utils/bin2bl.c:35:8: style: Variable 'font_end' can be declared as const array [constVariable] lagan20/src/utils/bin2bl.c:36:8: style: Variable 'status_start' can be declared as const array [constVariable] lagan20/src/utils/bin2bl.c:37:8: style: Variable 'status_end' can be declared as const array [constVariable] lagan20/src/utils/bin2bl.c:38:8: style: Variable 'dash' can be declared as const array [constVariable] lagan20/src/utils/bin2mf.c:22:17: error: Memory leak: seq1 [memleak] lagan20/src/utils/bin2mf.c:22:17: error: Memory leak: seq2 [memleak] lagan20/src/utils/bin2mf.c:26:5: error: Memory leak: seq1 [memleak] lagan20/src/utils/bin2mf.c:26:5: error: Memory leak: seq2 [memleak] lagan20/src/utils/bin2mf.c:42:7: error: Common realloc mistake: 'seq1' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/bin2bl.c:22:7: style: Variable 'width' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/bin2mf.c:43:7: error: Common realloc mistake: 'seq2' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/prolagan.c:176:13: style: Condition 'i>0' is always true [knownConditionTrueFalse] lagan20/src/prolagan.c:175:16: note: Assuming that condition 'i>0' is not redundant lagan20/src/prolagan.c:176:13: note: Condition 'i>0' is always true lagan20/src/prolagan.c:652:24: style: Condition 'treestr[i]==')'' is always false [knownConditionTrueFalse] lagan20/src/prolagan.c:93:9: warning: fprintf format string requires 1 parameter but 2 are given. [wrongPrintfScanfArgNum] lagan20/src/prolagan.c:126:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/prolagan.c:78:5: error: Memory leak: res [memleak] lagan20/src/prolagan.c:78:5: error: Memory leak: myseq [memleak] lagan20/src/prolagan.c:982:53: error: Memory leak: seqs [memleak] lagan20/src/prolagan.c:98:9: error: Common realloc mistake: 'res' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/prolagan.c:76:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:70:29: note: Assuming allocation function fails lagan20/src/prolagan.c:70:15: note: Assignment 'res=(char*)malloc(sizeof(char)*2)', assigned value is 0 lagan20/src/prolagan.c:76:3: note: Null pointer dereference lagan20/src/prolagan.c:126:21: warning: If memory allocation fails, then there is a possible null pointer dereference: first_word [nullPointerOutOfMemory] lagan20/src/prolagan.c:125:30: note: Assuming allocation function fails lagan20/src/prolagan.c:125:16: note: Assignment 'first_word=(char*)malloc((len+1)*sizeof(char))', assigned value is 0 lagan20/src/prolagan.c:126:21: note: Null pointer dereference lagan20/src/prolagan.c:127:24: warning: If memory allocation fails, then there is a possible null pointer dereference: first_word [nullPointerOutOfMemory] lagan20/src/prolagan.c:125:30: note: Assuming allocation function fails lagan20/src/prolagan.c:125:16: note: Assignment 'first_word=(char*)malloc((len+1)*sizeof(char))', assigned value is 0 lagan20/src/prolagan.c:127:24: note: Null pointer dereference lagan20/src/prolagan.c:164:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:214:23: note: Assuming condition is false lagan20/src/prolagan.c:218:24: note: Calling function 'appendAlignProfile', 1st argument 'res' value is 0 lagan20/src/prolagan.c:164:3: note: Null pointer dereference lagan20/src/utils/bin2mf.c:14:8: style: Variable 'bases' can be declared as const array [constVariable] lagan20/src/prolagan.c:164:13: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:214:23: note: Assuming condition is false lagan20/src/prolagan.c:218:24: note: Calling function 'appendAlignProfile', 1st argument 'res' value is 0 lagan20/src/prolagan.c:164:13: note: Null pointer dereference lagan20/src/prolagan.c:165:17: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:214:23: note: Assuming condition is false lagan20/src/prolagan.c:218:24: note: Calling function 'appendAlignProfile', 1st argument 'res' value is 0 lagan20/src/prolagan.c:165:17: note: Null pointer dereference lagan20/src/prolagan.c:191:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:191:3: note: Null pointer dereference lagan20/src/prolagan.c:192:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:192:3: note: Null pointer dereference lagan20/src/prolagan.c:193:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:193:3: note: Null pointer dereference lagan20/src/prolagan.c:194:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:194:3: note: Null pointer dereference lagan20/src/prolagan.c:195:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:195:3: note: Null pointer dereference lagan20/src/prolagan.c:196:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:196:3: note: Null pointer dereference lagan20/src/prolagan.c:200:9: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:200:9: note: Null pointer dereference lagan20/src/prolagan.c:214:10: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:214:10: note: Null pointer dereference lagan20/src/prolagan.c:267:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/prolagan.c:264:23: note: Assuming allocation function fails lagan20/src/prolagan.c:264:10: note: Assignment 'tt=(struct HitLocationList*)malloc(sizeof(struct HitLocationList))', assigned value is 0 lagan20/src/prolagan.c:267:5: note: Null pointer dereference lagan20/src/prolagan.c:363:9: warning: If memory allocation fails, then there is a possible null pointer dereference: array [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:426:24: note: Calling function 'findBestChain', 1st argument 'myptrs' value is 0 lagan20/src/prolagan.c:363:9: note: Null pointer dereference lagan20/src/prolagan.c:417:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:417:5: note: Null pointer dereference lagan20/src/prolagan.c:418:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:418:5: note: Null pointer dereference lagan20/src/prolagan.c:419:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:419:5: note: Null pointer dereference lagan20/src/prolagan.c:420:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:420:5: note: Null pointer dereference lagan20/src/prolagan.c:421:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:421:5: note: Null pointer dereference lagan20/src/prolagan.c:422:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:422:5: note: Null pointer dereference lagan20/src/prolagan.c:425:9: warning: If memory allocation fails, then there is a possible null pointer dereference: myptrs [nullPointerOutOfMemory] lagan20/src/prolagan.c:415:27: note: Assuming allocation function fails lagan20/src/prolagan.c:415:12: note: Assignment 'myptrs=(struct hptr*)malloc(sizeof(struct hptr)*numhits*2)', assigned value is 0 lagan20/src/prolagan.c:425:9: note: Null pointer dereference lagan20/src/prolagan.c:108:16: style: The comparison 'seqstart > 0' is always false. [knownConditionTrueFalse] lagan20/src/prolagan.c:68:16: note: 'seqstart' is assigned value '0' here. lagan20/src/prolagan.c:108:16: note: The comparison 'seqstart > 0' is always false. lagan20/src/prolagan.c:110:15: style: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. [duplicateExpression] lagan20/src/prolagan.c:69:14: note: 'seqend' is assigned value '0' here. lagan20/src/prolagan.c:68:16: note: 'seqstart' is assigned value '0' here. lagan20/src/prolagan.c:110:15: note: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. lagan20/src/prolagan.c:111:21: style: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. [duplicateExpression] lagan20/src/prolagan.c:69:14: note: 'seqend' is assigned value '0' here. lagan20/src/prolagan.c:68:16: note: 'seqstart' is assigned value '0' here. lagan20/src/prolagan.c:111:21: note: Same expression on both sides of '-' because 'seqend' and 'seqstart' represent the same value. lagan20/src/prolagan.c:120:23: style: Parameter 'str' can be declared as pointer to const [constParameterPointer] lagan20/src/prolagan.c:120:34: style: Parameter 'word' can be declared as pointer to const [constParameterPointer] lagan20/src/prolagan.c:244:29: style: Parameter 'fname' can be declared as pointer to const [constParameterPointer] lagan20/src/prolagan.c:246:29: style: Variable 'first' can be declared as pointer to const [constVariablePointer] lagan20/src/prolagan.c:293:9: style: Variable 'name1' can be declared as pointer to const [constVariablePointer] lagan20/src/prolagan.c:293:17: style: Variable 'name2' can be declared as pointer to const [constVariablePointer] lagan20/src/prolagan.c:294:9: style: Variable 'endpnt' can be declared as pointer to const [constVariablePointer] lagan20/src/prolagan.c:340:40: style: Parameter 'myseq' can be declared as pointer to const [constParameterPointer] lagan20/src/prolagan.c:462:52: style: Parameter 'index' can be declared as pointer to const [constParameterPointer] lagan20/src/prolagan.c:89:32: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] lagan20/src/utils/cextract.c:92:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/prolagan.c:695:10: warning: Uninitialized variables: stack.num, stack.index, stack.score, stack.algnlen, stack.numseq, stack.algn, stack.dirty, stack.nextalign [uninitvar] lagan20/src/prolagan.c:674:12: note: Assuming condition is false lagan20/src/prolagan.c:686:14: note: Assuming condition is true lagan20/src/prolagan.c:695:10: note: Uninitialized variables: stack.num, stack.index, stack.score, stack.algnlen, stack.numseq, stack.algn, stack.dirty, stack.nextalign lagan20/src/prolagan.c:41:10: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:41:7: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:163:9: style: Unused variable: j [unusedVariable] lagan20/src/prolagan.c:246:23: style: Variable 'tt' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:246:35: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:246:29: style: Variable 'first' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:298:13: style: Variable 'flip' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:296:10: style: Unused variable: temp [unusedVariable] lagan20/src/prolagan.c:298:8: style: Variable 'flip' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:395:19: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:392:7: style: Unused variable: len [unusedVariable] lagan20/src/prolagan.c:394:15: style: Unused variable: t2 [unusedVariable] lagan20/src/prolagan.c:394:20: style: Unused variable: t3 [unusedVariable] lagan20/src/prolagan.c:395:7: style: Unused variable: i [unusedVariable] lagan20/src/prolagan.c:395:10: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:539:36: style: Unused variable: uni [unusedVariable] lagan20/src/prolagan.c:585:12: style: Unused variable: oldscore [unusedVariable] lagan20/src/prolagan.c:587:10: style: Unused variable: readd [unusedVariable] lagan20/src/prolagan.c:630:16: style: Unused variable: j [unusedVariable] lagan20/src/prolagan.c:956:16: style: Variable 'j' is assigned a value that is never used. [unreadVariable] lagan20/src/prolagan.c:954:14: style: Unused variable: seqfile [unusedVariable] lagan20/src/prolagan.c:960:8: style: Unused variable: command [unusedVariable] lagan20/src/utils/contigorder.c:15:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/contigorder.c:52:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/contigorder.c:185:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/contigorder.c:330:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/cextract.c:10:22: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/cstat.c:46:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/cstat.c:69:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/cstat.c:237:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/dotplot.cpp:15:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/cstat.c:156:69: style: Condition '0==myal->numseq-1' is always false [knownConditionTrueFalse] lagan20/src/utils/cstat.c:155:22: note: Assuming that condition 'myal->numseq==2' is not redundant lagan20/src/utils/cstat.c:156:69: note: Condition '0==myal->numseq-1' is always false lagan20/src/utils/cstat.c:157:69: style: Condition '1==myal->numseq-1' is always true [knownConditionTrueFalse] lagan20/src/utils/cstat.c:155:22: note: Assuming that condition 'myal->numseq==2' is not redundant lagan20/src/utils/cstat.c:157:69: note: Condition '1==myal->numseq-1' is always true lagan20/src/utils/cstat.c:209:2: error: Common realloc mistake: 'first' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/cstat.c:210:2: error: Common realloc mistake: 'last' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/cstat.c:107:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/cstat.c:106:31: note: Assuming allocation function fails lagan20/src/utils/cstat.c:106:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/utils/cstat.c:107:3: note: Null pointer dereference lagan20/src/utils/cstat.c:109:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/cstat.c:106:31: note: Assuming allocation function fails lagan20/src/utils/cstat.c:106:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/utils/cstat.c:109:5: note: Null pointer dereference lagan20/src/utils/cstat.c:111:5: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/cstat.c:106:31: note: Assuming allocation function fails lagan20/src/utils/cstat.c:106:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/utils/cstat.c:111:5: note: Null pointer dereference lagan20/src/utils/cstat.c:113:7: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/cstat.c:106:31: note: Assuming allocation function fails lagan20/src/utils/cstat.c:106:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/utils/cstat.c:113:7: note: Null pointer dereference lagan20/src/utils/cstat.c:142:31: style: Parameter 'first' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/cstat.c:142:43: style: Parameter 'last' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/cstat.c:77:54: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] lagan20/src/utils/cstat.c:25:7: style: struct member 'pair_ints::s' is never used. [unusedStructMember] lagan20/src/utils/cstat.c:26:7: style: struct member 'pair_ints::e' is never used. [unusedStructMember] lagan20/src/utils/cstat.c:234:7: style: Unused variable: i [unusedVariable] lagan20/src/utils/fa2xfa.c:20:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/fa2xfa.c:99:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/contigorder.c:15:5: error: fprintf format string requires 1 parameter but only 0 are given. [wrongPrintfScanfArgNum] lagan20/src/utils/contigorder.c:52:5: error: fprintf format string requires 1 parameter but only 0 are given. [wrongPrintfScanfArgNum] lagan20/src/utils/fa2xfa.c:24:22: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/fa2xfa.c:81:18: style: Variable 'pos' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/fa2xfa.c:81:38: style: Variable 'j' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/fa2xfa.c:81:14: style: Variable 'pos' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/fa2xfa.c:81:36: style: Variable 'j' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/contigorder.c:10:25: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/contigorder.c:36:23: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/contigorder.c:116:48: style: Parameter 'cols' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/contigorder.c:151:42: style: Parameter 'cols' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/contigorder.c:151:66: style: Parameter 'first' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/contigorder.c:151:78: style: Parameter 'last' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/contigorder.c:244:10: warning: Uninitialized variable: bestState [uninitvar] lagan20/src/utils/contigorder.c:206:17: note: Assuming condition is false lagan20/src/utils/contigorder.c:244:10: note: Uninitialized variable: bestState lagan20/src/utils/contigorder.c:176:30: style: Unused variable: ptr [unusedVariable] lagan20/src/utils/getbounds.c:37:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/dotplot.cpp:21:13: style: Condition 'name1==NULL' is always true [knownConditionTrueFalse] lagan20/src/utils/dotplot.cpp:9:17: note: Assignment 'name1=NULL', assigned value is 0 lagan20/src/utils/dotplot.cpp:14:12: note: Assuming condition is false lagan20/src/utils/dotplot.cpp:21:13: note: Condition 'name1==NULL' is always true lagan20/src/utils/dotplot.cpp:28:17: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: file [nullPointerOutOfResources] lagan20/src/utils/dotplot.cpp:27:16: note: Assuming allocation function fails lagan20/src/utils/dotplot.cpp:27:16: note: Assignment 'file=fopen(argv[1],"r")', assigned value is 0 lagan20/src/utils/dotplot.cpp:28:17: note: Null pointer dereference lagan20/src/utils/dotplot.cpp:52:17: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: file [nullPointerOutOfResources] lagan20/src/utils/dotplot.cpp:43:16: note: Assuming allocation function fails lagan20/src/utils/dotplot.cpp:43:16: note: Assignment 'file=fopen(argv[1],"r")', assigned value is 0 lagan20/src/utils/dotplot.cpp:52:17: note: Null pointer dereference lagan20/src/utils/dotplot.cpp:79:17: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: file [nullPointerOutOfResources] lagan20/src/utils/dotplot.cpp:78:16: note: Assuming allocation function fails lagan20/src/utils/dotplot.cpp:78:16: note: Assignment 'file=fopen(argv[1],"r")', assigned value is 0 lagan20/src/utils/dotplot.cpp:79:17: note: Null pointer dereference lagan20/src/utils/dotplot.cpp:9:9: style: Variable 'name1' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/dotplot.cpp:10:9: style: Variable 'name2' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/dotplot.cpp:24:6: style: Variable 'pa' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/dotplot.cpp:25:6: style: Variable 'pb' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/dotplot.cpp:70:5: style: Variable 'pa' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/dotplot.cpp:71:5: style: Variable 'pb' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getcontigpos.c:83:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/dotplot.cpp:84:6: style: Variable 'PAD' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/dotplot.cpp:93:5: style: Variable 'pa' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/dotplot.cpp:94:5: style: Variable 'pb' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getlength.c:15:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/getbounds.c:12:22: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/getbounds.c:55:7: style: Variable 'm1e' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getbounds.c:81:9: style: Variable 'S2B' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getbounds.c:82:9: style: Variable 'S2E' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getbounds.c:32:27: style: Unused variable: ext [unusedVariable] lagan20/src/utils/getcontigpos.c:10:22: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/getcontigpos.c:66:41: style: Variable 'written' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getcontigpos.c:66:48: style: Variable 'j' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getcontigpos.c:66:33: style: Variable 'written' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/getcontigpos.c:66:46: style: Variable 'j' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/rc.c:37:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar] lagan20/src/utils/rc.c:38:5: error: Memory leak: res [memleak] lagan20/src/utils/overlay.c:104:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/overlay.c:164:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/rc.c:53:2: error: Common realloc mistake: 'res' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/overlay.c:183:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/overlay.c:201:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/overlay.c:217:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] lagan20/src/utils/overlay.c:236:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/rc.c:49:32: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] lagan20/src/utils/rc.c:9:9: style: struct member 'Sequence::lets' is never used. [unusedStructMember] lagan20/src/utils/rc.c:10:7: style: struct member 'Sequence::numlets' is never used. [unusedStructMember] lagan20/src/utils/rc.c:11:9: style: struct member 'Sequence::name' is never used. [unusedStructMember] lagan20/src/utils/rc.c:12:9: style: struct member 'Sequence::rptr' is never used. [unusedStructMember] lagan20/src/utils/overlay.c:127:9: error: Common realloc mistake: 'res' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/overlay.c:46:5: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:46:5: note: Null pointer dereference lagan20/src/utils/overlay.c:46:19: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_LET [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:41:28: note: Assuming allocation function fails lagan20/src/utils/overlay.c:41:13: note: Assignment 'DNA_LET=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:46:19: note: Null pointer dereference lagan20/src/utils/overlay.c:46:32: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:46:32: note: Null pointer dereference lagan20/src/utils/overlay.c:49:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_LET [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:41:28: note: Assuming allocation function fails lagan20/src/utils/overlay.c:41:13: note: Assignment 'DNA_LET=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:49:3: note: Null pointer dereference lagan20/src/utils/overlay.c:50:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_LET [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:41:28: note: Assuming allocation function fails lagan20/src/utils/overlay.c:41:13: note: Assignment 'DNA_LET=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:50:3: note: Null pointer dereference lagan20/src/utils/overlay.c:51:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_LET [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:41:28: note: Assuming allocation function fails lagan20/src/utils/overlay.c:41:13: note: Assignment 'DNA_LET=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:51:3: note: Null pointer dereference lagan20/src/utils/overlay.c:52:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_LET [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:41:28: note: Assuming allocation function fails lagan20/src/utils/overlay.c:41:13: note: Assignment 'DNA_LET=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:52:3: note: Null pointer dereference lagan20/src/utils/overlay.c:53:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:53:3: note: Null pointer dereference lagan20/src/utils/overlay.c:54:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:54:3: note: Null pointer dereference lagan20/src/utils/overlay.c:55:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:55:3: note: Null pointer dereference lagan20/src/utils/overlay.c:56:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:56:3: note: Null pointer dereference lagan20/src/utils/overlay.c:57:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:57:3: note: Null pointer dereference lagan20/src/utils/overlay.c:58:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:58:3: note: Null pointer dereference lagan20/src/utils/overlay.c:59:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:59:3: note: Null pointer dereference lagan20/src/utils/overlay.c:60:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:60:3: note: Null pointer dereference lagan20/src/utils/overlay.c:61:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:61:3: note: Null pointer dereference lagan20/src/utils/overlay.c:62:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:62:3: note: Null pointer dereference lagan20/src/utils/overlay.c:63:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:63:3: note: Null pointer dereference lagan20/src/utils/overlay.c:64:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:64:3: note: Null pointer dereference lagan20/src/utils/overlay.c:65:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:65:3: note: Null pointer dereference lagan20/src/utils/overlay.c:66:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:66:3: note: Null pointer dereference lagan20/src/utils/overlay.c:67:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:67:3: note: Null pointer dereference lagan20/src/utils/overlay.c:68:3: warning: If memory allocation fails, then there is a possible null pointer dereference: DNA_PRINT [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:42:30: note: Assuming allocation function fails lagan20/src/utils/overlay.c:42:15: note: Assignment 'DNA_PRINT=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:68:3: note: Null pointer dereference lagan20/src/utils/overlay.c:69:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:69:3: note: Null pointer dereference lagan20/src/utils/overlay.c:70:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:70:3: note: Null pointer dereference lagan20/src/utils/overlay.c:71:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:71:3: note: Null pointer dereference lagan20/src/utils/overlay.c:72:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:72:3: note: Null pointer dereference lagan20/src/utils/overlay.c:73:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:73:3: note: Null pointer dereference lagan20/src/utils/overlay.c:74:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:74:3: note: Null pointer dereference lagan20/src/utils/overlay.c:75:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:75:3: note: Null pointer dereference lagan20/src/utils/overlay.c:76:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:76:3: note: Null pointer dereference lagan20/src/utils/overlay.c:77:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:77:3: note: Null pointer dereference lagan20/src/utils/overlay.c:78:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:78:3: note: Null pointer dereference lagan20/src/utils/overlay.c:79:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:79:3: note: Null pointer dereference lagan20/src/utils/overlay.c:80:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:80:3: note: Null pointer dereference lagan20/src/utils/overlay.c:81:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:81:3: note: Null pointer dereference lagan20/src/utils/overlay.c:82:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:82:3: note: Null pointer dereference lagan20/src/utils/overlay.c:83:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:83:3: note: Null pointer dereference lagan20/src/utils/overlay.c:84:3: warning: If memory allocation fails, then there is a possible null pointer dereference: NUM_ONES [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:43:29: note: Assuming allocation function fails lagan20/src/utils/overlay.c:43:14: note: Assignment 'NUM_ONES=(char*)malloc(sizeof(char)*0x10)', assigned value is 0 lagan20/src/utils/overlay.c:84:3: note: Null pointer dereference lagan20/src/utils/overlay.c:90:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:89:26: note: Assuming allocation function fails lagan20/src/utils/overlay.c:89:14: note: Assignment 'res=(struct seq*)malloc(sizeof(struct seq))', assigned value is 0 lagan20/src/utils/overlay.c:90:3: note: Null pointer dereference lagan20/src/utils/overlay.c:91:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:89:26: note: Assuming allocation function fails lagan20/src/utils/overlay.c:89:14: note: Assignment 'res=(struct seq*)malloc(sizeof(struct seq))', assigned value is 0 lagan20/src/utils/overlay.c:91:3: note: Null pointer dereference lagan20/src/utils/overlay.c:92:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:89:26: note: Assuming allocation function fails lagan20/src/utils/overlay.c:89:14: note: Assignment 'res=(struct seq*)malloc(sizeof(struct seq))', assigned value is 0 lagan20/src/utils/overlay.c:92:3: note: Null pointer dereference lagan20/src/utils/overlay.c:93:3: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/utils/overlay.c:89:26: note: Assuming allocation function fails lagan20/src/utils/overlay.c:89:14: note: Assignment 'res=(struct seq*)malloc(sizeof(struct seq))', assigned value is 0 lagan20/src/utils/overlay.c:93:3: note: Null pointer dereference lagan20/src/utils/overlay.c:160:29: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/overlay.c:173:9: style: Variable 'filename' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/overlay.c:214:8: style: Variable 'a' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/overlay.c:118:32: warning: Storing fgetc() return value in char variable and then comparing with EOF. [checkCastIntToCharAndBack] lagan20/src/utils/overlay.c:101:30: style: Unused variable: tt [unusedVariable] lagan20/src/utils/overlay.c:181:9: style: Variable 'myn' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/overlay.c:176:10: style: Unused variable: j [unusedVariable] lagan20/src/utils/overlay.c:176:13: style: Unused variable: kmer [unusedVariable] lagan20/src/utils/overlay.c:176:19: style: Unused variable: breaker [unusedVariable] lagan20/src/utils/overlay.c:230:8: style: Unused variable: string_tree [unusedVariable] lagan20/src/utils/overlay.c:231:7: style: Unused variable: moved [unusedVariable] lagan20/src/utils/overlay.c:232:9: style: Unused variable: ttree [unusedVariable] lagan20/src/utils/overlay.c:232:16: style: Unused variable: test [unusedVariable] lagan20/src/utils/scorealign.c:406:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/scorealign.c:459:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/seqmerge.c:13:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/seqmerge.c:33:6: style: Suspicious condition (bitwise operator + comparison); Clarify expression with parentheses. [clarifyCondition] lagan20/src/utils/seqmerge.c:33:15: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition] lagan20/src/utils/scorecontigs.c:57:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/scorecontigs.c:83:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/scorecontigs.c:119:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/scorecontigs.c:364:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] lagan20/src/utils/scorealign.c:246:13: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/utils/scorealign.c:288:7: error: Common realloc mistake: 'buffer' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/scorealign.c:325:5: error: Common realloc mistake: 'seqs' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/scorealign.c:326:5: error: Common realloc mistake: 'seqid' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/scorealign.c:327:5: error: Common realloc mistake: 'seqstart' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/scorealign.c:328:5: error: Common realloc mistake: 'seqend' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/scorealign.c:329:5: error: Common realloc mistake: 'seqdir' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/scorealign.c:330:5: error: Common realloc mistake: 'seqcomment' nulled but not freed upon failure [memleakOnRealloc] lagan20/src/utils/scorealign.c:55:22: style: Parameter 'seq1' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorealign.c:55:34: style: Parameter 'seq2' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorealign.c:139:21: style: Parameter 'orig1' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorealign.c:139:34: style: Parameter 'orig2' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorealign.c:242:29: style: Parameter 'line' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorealign.c:382:9: style: Variable 'alpha' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/scorealign.c:398:29: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorealign.c:402:9: style: Variable 'lagan_dir' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/scorealign.c:434:25: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorealign.c:262:15: style: Variable 'prevch' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/scorealign.c:291:12: style: Variable 'prevch' is assigned a value that is never used. [unreadVariable] lagan20/src/utils/scorealign.c:310:7: style: Unused variable: i [unusedVariable] lagan20/src/utils/scorealign.c:353:10: style: Unused variable: j [unusedVariable] lagan20/src/utils/scorecontigs.c:384:9: warning: fscanf() without field width limits can crash with huge input data. [invalidscanf] lagan20/src/utils/scorecontigs.c:60:12: style: Redundant initialization for 'currchar'. The initialized value is overwritten before it is read. [redundantInitialization] lagan20/src/utils/scorecontigs.c:50:17: note: currchar is initialized lagan20/src/utils/scorecontigs.c:60:12: note: currchar is overwritten lagan20/src/utils/scorecontigs.c:114:27: style: Parameter 'filename' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorecontigs.c:144:10: style: Variable 'myal' can be declared as pointer to const [constVariablePointer] lagan20/src/utils/scorecontigs.c:238:46: style: Parameter 'offs' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorecontigs.c:261:45: style: Parameter 'score' can be declared as pointer to const [constParameterPointer] lagan20/src/utils/scorecontigs.c:344:13: style: Unused variable: k [unusedVariable] diff: head lagan20/src/anchors.c:171:17: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] head lagan20/src/anchors.c:49:7: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] head lagan20/src/ancseq.cpp:169:8: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:168:25: note: Assuming allocation function fails lagan20/src/ancseq.cpp:168:12: note: Assignment 'buf=(char*)std::malloc(length*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:169:8: note: Null pointer dereference head lagan20/src/ancseq.cpp:180:10: warning: If memory allocation fails, then there is a possible null pointer dereference: rev [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:178:26: note: Assuming allocation function fails lagan20/src/ancseq.cpp:178:13: note: Assignment 'rev=(char*)std::malloc(length*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:180:10: note: Null pointer dereference head lagan20/src/ancseq.cpp:251:9: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:250:25: note: Assuming allocation function fails lagan20/src/ancseq.cpp:250:12: note: Assignment 'buf=(char*)std::malloc(size*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:251:9: note: Null pointer dereference head lagan20/src/ancseq.cpp:253:10: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:250:25: note: Assuming allocation function fails lagan20/src/ancseq.cpp:250:12: note: Assignment 'buf=(char*)std::malloc(size*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:253:10: note: Null pointer dereference head lagan20/src/ancseq.cpp:364:11: warning: If memory allocation fails, then there is a possible null pointer dereference: cons [nullPointerOutOfMemory] lagan20/src/ancseq.cpp:363:22: note: Assuming allocation function fails lagan20/src/ancseq.cpp:363:9: note: Assignment 'cons=(char*)std::malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/ancseq.cpp:364:11: note: Null pointer dereference head lagan20/src/ancseq.cpp:380:6: style: Variable 'length' is assigned a value that is never used. [unreadVariable] head lagan20/src/ancseq.cpp:403:6: style: Variable 'length' is assigned a value that is never used. [unreadVariable] head lagan20/src/ancseqrest.cpp:265:8: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory] lagan20/src/ancseqrest.cpp:264:25: note: Assuming allocation function fails lagan20/src/ancseqrest.cpp:264:12: note: Assignment 'buf=(char*)std::malloc(length*sizeof(char))', assigned value is 0 lagan20/src/ancseqrest.cpp:265:8: note: Null pointer dereference head lagan20/src/diagmatrix.c:30:26: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:30:26: note: Null pointer dereference head lagan20/src/diagmatrix.c:30:47: warning: If memory allocation fails, then there is a possible null pointer dereference: trgt [nullPointerOutOfMemory] lagan20/src/diagmatrix.c:20:29: note: Assuming allocation function fails lagan20/src/diagmatrix.c:20:16: note: Assignment 'trgt=(struct dmat*)malloc(sizeof(struct dmat))', assigned value is 0 lagan20/src/diagmatrix.c:30:47: note: Null pointer dereference head lagan20/src/faindex.cpp:43:8: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory] lagan20/src/faindex.cpp:42:25: note: Assuming allocation function fails lagan20/src/faindex.cpp:42:12: note: Assignment 'seq=(char*)std::malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/faindex.cpp:43:8: note: Null pointer dereference head lagan20/src/faindex.cpp:54:8: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory] lagan20/src/faindex.cpp:53:25: note: Assuming allocation function fails lagan20/src/faindex.cpp:53:12: note: Assignment 'seq=(char*)std::malloc(ind.length*sizeof(char))', assigned value is 0 lagan20/src/faindex.cpp:54:8: note: Null pointer dereference head lagan20/src/fchaos.c:1039:16: warning: If memory allocation fails, then there is a possible null pointer dereference: s1arr [nullPointerOutOfMemory] lagan20/src/fchaos.c:1035:25: note: Assuming allocation function fails lagan20/src/fchaos.c:1035:11: note: Assignment 's1arr=(int*)malloc(sizeof(int)*(length+1))', assigned value is 0 lagan20/src/fchaos.c:1039:16: note: Null pointer dereference head lagan20/src/fchaos.c:1040:23: warning: If memory allocation fails, then there is a possible null pointer dereference: s2arr [nullPointerOutOfMemory] lagan20/src/fchaos.c:1036:25: note: Assuming allocation function fails lagan20/src/fchaos.c:1036:11: note: Assignment 's2arr=(int*)malloc(sizeof(int)*(length+1))', assigned value is 0 lagan20/src/fchaos.c:1040:23: note: Null pointer dereference head lagan20/src/fchaos.c:401:10: style: Variable 'd1' is assigned a value that is never used. [unreadVariable] head lagan20/src/fchaos.c:401:16: style: Variable 'd2' is assigned a value that is never used. [unreadVariable] head lagan20/src/fchaos.c:440:7: style: Variable 'doneset' is assigned a value that is never used. [unreadVariable] head lagan20/src/fchaos.c:542:9: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] head lagan20/src/fchaos.c:543:24: style: Variable 'bestdbaseloc' is assigned a value that is never used. [unreadVariable] head lagan20/src/fchaos.c:543:7: style: Variable 'bestqueryloc' is assigned a value that is never used. [unreadVariable] head lagan20/src/global.c:46:17: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:46:17: note: Null pointer dereference head lagan20/src/global.c:51:17: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:51:17: note: Null pointer dereference head lagan20/src/global.c:57:21: warning: If memory allocation fails, then there is a possible null pointer dereference: N [nullPointerOutOfMemory] lagan20/src/global.c:37:27: note: Assuming allocation function fails lagan20/src/global.c:37:13: note: Assignment 'N=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:57:21: note: Null pointer dereference head lagan20/src/global.c:58:21: warning: If memory allocation fails, then there is a possible null pointer dereference: O [nullPointerOutOfMemory] lagan20/src/global.c:38:27: note: Assuming allocation function fails lagan20/src/global.c:38:13: note: Assignment 'O=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:58:21: note: Null pointer dereference head lagan20/src/global.c:59:21: warning: If memory allocation fails, then there is a possible null pointer dereference: M [nullPointerOutOfMemory] lagan20/src/global.c:36:27: note: Assuming allocation function fails lagan20/src/global.c:36:13: note: Assignment 'M=(int*)malloc(sizeof(int)*(end1-start1+1)*(end2-start2+1))', assigned value is 0 lagan20/src/global.c:59:21: note: Null pointer dereference head lagan20/src/makecons.cpp:87:10: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory] lagan20/src/makecons.cpp:207:21: note: Assuming allocation function fails lagan20/src/makecons.cpp:207:8: note: Assignment 'cons=(char*)std::malloc(sizeof(char)*len)', assigned value is 0 lagan20/src/makecons.cpp:211:16: note: Calling function 'writeSeq', 2nd argument 'cons' value is 0 lagan20/src/makecons.cpp:87:10: note: Null pointer dereference head lagan20/src/mlagan.c:161:29: style: Variable 'first' is assigned a value that is never used. [unreadVariable] head lagan20/src/mlagan.c:213:8: style: Variable 'flip' is assigned a value that is never used. [unreadVariable] head lagan20/src/mlagan.c:310:10: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] head lagan20/src/mlagan.c:38:7: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:103:19: style: Variable 'isfrst' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1465:13: style: Variable 's2' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1465:7: style: Variable 's1' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1466:7: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1524:13: style: Variable 's2' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1524:7: style: Variable 's1' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1525:7: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1552:13: style: Variable 's2' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1552:7: style: Variable 's1' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:1553:7: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:357:9: style: Variable 'first' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:358:6: style: Variable 'second' is assigned a value that is never used. [unreadVariable] head lagan20/src/multial.c:381:10: style: Variable 'n' is assigned a value that is never used. [unreadVariable] head lagan20/src/order.c:237:38: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/order.c:233:23: note: Assuming allocation function fails lagan20/src/order.c:233:10: note: Assignment 'tt=(struct hll*)malloc(sizeof(struct hll))', assigned value is 0 lagan20/src/order.c:237:38: note: Null pointer dereference head lagan20/src/order.c:238:31: warning: If memory allocation fails, then there is a possible null pointer dereference: tt [nullPointerOutOfMemory] lagan20/src/order.c:233:23: note: Assuming allocation function fails lagan20/src/order.c:233:10: note: Assignment 'tt=(struct hll*)malloc(sizeof(struct hll))', assigned value is 0 lagan20/src/order.c:238:31: note: Null pointer dereference head lagan20/src/order.c:560:9: style: Variable 'first' is assigned a value that is never used. [unreadVariable] head lagan20/src/order.c:561:6: style: Variable 'second' is assigned a value that is never used. [unreadVariable] head lagan20/src/order.c:586:10: style: Variable 'n' is assigned a value that is never used. [unreadVariable] head lagan20/src/order.c:773:27: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] head lagan20/src/order.c:773:7: style: Variable 'nm' is assigned a value that is never used. [unreadVariable] head lagan20/src/order.c:805:27: style: Variable 'nlets' is assigned a value that is never used. [unreadVariable] head lagan20/src/order.c:805:7: style: Variable 'nm' is assigned a value that is never used. [unreadVariable] head lagan20/src/prolagan.c:164:13: warning: If memory allocation fails, then there is a possible null pointer dereference: res [nullPointerOutOfMemory] lagan20/src/prolagan.c:190:32: note: Assuming allocation function fails lagan20/src/prolagan.c:190:16: note: Assignment 'res=(struct align*)malloc(sizeof(struct align))', assigned value is 0 lagan20/src/prolagan.c:214:23: note: Assuming condition is false lagan20/src/prolagan.c:218:24: note: Calling function 'appendAlignProfile', 1st argument 'res' value is 0 lagan20/src/prolagan.c:164:13: note: Null pointer dereference head lagan20/src/prolagan.c:246:29: style: Variable 'first' is assigned a value that is never used. [unreadVariable] head lagan20/src/prolagan.c:298:8: style: Variable 'flip' is assigned a value that is never used. [unreadVariable] head lagan20/src/prolagan.c:395:10: style: Variable 'bestscore' is assigned a value that is never used. [unreadVariable] head lagan20/src/prolagan.c:41:7: style: Variable 'jt' is assigned a value that is never used. [unreadVariable] head lagan20/src/utils/fa2xfa.c:81:14: style: Variable 'pos' is assigned a value that is never used. [unreadVariable] head lagan20/src/utils/fa2xfa.c:81:36: style: Variable 'j' is assigned a value that is never used. [unreadVariable] head lagan20/src/utils/getcontigpos.c:66:33: style: Variable 'written' is assigned a value that is never used. [unreadVariable] head lagan20/src/utils/getcontigpos.c:66:46: style: Variable 'j' is assigned a value that is never used. [unreadVariable] DONE