2026-05-04 07:58
ftp://ftp.de.debian.org/debian/pool/main/p/piler/piler_0~20140707.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 -j1
platform: Linux-6.12.85+deb13-amd64-x86_64-with-glibc2.41
python: 3.13.5
client-version: 1.3.70
compiler: g++ (20250906) 15.2.0
cppcheck: head 2.20.0
head-info: e5c4a73 (2026-05-01 11:10:43 +0200)
count: 259 248
elapsed-time: 2.5 2.1
head-timing-info:

old-timing-info:

head results:
annot.cpp:24:15: style: Local variable 'Annot' shadows outer function [shadowFunction]
piler2.h:144:6: note: Shadowed declaration
annot.cpp:24:15: note: Shadow variable
annot.cpp:11:11: style: Variable 'Reps' can be declared as pointer to const [constVariablePointer]
annotedge.cpp:24:15: style: Local variable 'Annot' shadows outer function [shadowFunction]
piler2.h:144:6: note: Shadowed declaration
annotedge.cpp:24:15: note: Shadow variable
annotedge.cpp:11:11: style: Variable 'Reps' can be declared as pointer to const [constVariablePointer]
cons.cpp:104:18: style: C-style pointer casting [cstyleCast]
contigs.cpp:163:30: warning: Either the condition '0==Contig' is redundant or there is possible null pointer dereference: Contig. [nullPointerRedundantCheck]
contigs.cpp:161:8: note: Assuming that condition '0==Contig' is not redundant
contigs.cpp:163:30: note: Null pointer dereference
contigs.cpp:52:23: style: C-style pointer casting [cstyleCast]
contigs.cpp:80:23: style: C-style pointer casting [cstyleCast]
contigs.cpp:128:14: style: C-style pointer casting [cstyleCast]
contigs.cpp:102:16: style: Variable 'Contig' can be declared as reference to const [constVariableReference]
contigs.cpp:135:16: style: Variable 'Contig' can be declared as reference to const [constVariableReference]
contigs.cpp:160:14: style: Variable 'Contig' can be declared as pointer to const [constVariablePointer]
contigs.cpp:102:23: style: Variable 'Contig' is assigned a value that is never used. [unreadVariable]
contigs.cpp:135:23: style: Variable 'Contig' is assigned a value that is never used. [unreadVariable]
crisp.cpp:82:33: style: C-style pointer casting [cstyleCast]
crisp.cpp:144:18: style: C-style pointer casting [cstyleCast]
crisp.cpp:145:18: style: C-style pointer casting [cstyleCast]
crisp.cpp:151:26: style: C-style pointer casting [cstyleCast]
crisp.cpp:152:26: style: C-style pointer casting [cstyleCast]
crisp.cpp:190:10: style: C-style pointer casting [cstyleCast]
crisp.cpp:228:17: style: C-style pointer casting [cstyleCast]
crisp.cpp:358:30: style: C-style pointer casting [cstyleCast]
crisp.cpp:359:22: style: C-style pointer casting [cstyleCast]
crisp.cpp:546:19: style: C-style pointer casting [cstyleCast]
crisp.cpp:396:6: style: Local variable 'PileCount' shadows outer variable [shadowVariable]
crisp.cpp:42:12: note: Shadowed declaration
crisp.cpp:396:6: note: Shadow variable
crisp.cpp:526:6: style: Local variable 'SeqLength' shadows outer variable [shadowVariable]
crisp.cpp:46:12: note: Shadowed declaration
crisp.cpp:526:6: note: Shadow variable
crisp.cpp:307:36: style: Parameter 'Pile' can be declared as reference to const [constParameterReference]
crisp.cpp:371:40: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
crisp.cpp:381:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
crisp.cpp:535:12: style: Variable 'Hit' can be declared as reference to const [constVariableReference]
crisp.cpp:626:20: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
crisp.cpp:628:15: style: Variable 'Pile' can be declared as reference to const [constVariableReference]
crisp.cpp:144:11: style: Variable 'Hit1' can be declared as pointer to const [constVariablePointer]
crisp.cpp:145:11: style: Variable 'Hit2' can be declared as pointer to const [constVariablePointer]
crisp.cpp:156:47: style: Parameter 'Images' can be declared as pointer to const [constParameterPointer]
crisp.cpp:188:20: style: Parameter 'PileIndexes' can be declared as pointer to const [constParameterPointer]
crisp.cpp:340:36: style: Parameter 'PartnersRev' can be declared as const array [constParameter]
crisp.cpp:502:12: style: Variable 'Fam' can be declared as pointer to const [constVariablePointer]
bitfuncs.h:12:33: style: Parameter 'BitVec' can be declared as pointer to const [constParameterPointer]
crisp.cpp:220:22: style: Variable 'TotalImageCount' is assigned a value that is never used. [unreadVariable]
crisp.cpp:226:19: style: Variable 'TotalImageCount' is assigned a value that is never used. [unreadVariable]
crisp.cpp:320:32: style: Variable 'PartnerImageLength' is assigned a value that is never used. [unreadVariable]
crisp.cpp:573:7: style: Variable 'Hits' is assigned a value that is never used. [unreadVariable]
crisp.cpp:583:14: style: Variable 'PileIndexes' is assigned a value that is never used. [unreadVariable]
findcc.cpp:116:34: style: Parameter 'Edges' can be declared as reference to const [constParameterReference]
findcc.cpp:121:13: style: Variable 'Edge' can be declared as reference to const [constVariableReference]
findcc.cpp:171:13: style: Variable 'Edge' can be declared as reference to const [constVariableReference]
findcc.cpp:210:19: style: Variable 'Neighbor' can be declared as reference to const [constVariableReference]
findcc.cpp:31:35: style: Parameter 'Nodes' can be declared as pointer to const [constParameterPointer]
findcc.cpp:75:12: style: Variable 'Head' can be declared as pointer to const [constVariablePointer]
findcc.cpp:104:36: style: Parameter 'Node' can be declared as pointer to const [constParameterPointer]
findcc.cpp:75:17: style: Variable 'Head' is assigned a value that is never used. [unreadVariable]
gff.cpp:45:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gff.cpp:17:9: style: Variable 'End' can be declared as pointer to const [constVariablePointer]
gff.cpp:39:9: style: Variable 'Ok' can be declared as pointer to const [constVariablePointer]
gff.cpp:37:14: style: Variable 'TAB' is assigned a value that is never used. [unreadVariable]
gff2.cpp:120:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
gff2.cpp:25:35: warning: Either the condition '0==ptrPiles' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
gff2.cpp:22:8: note: Assuming that condition '0==ptrPiles' is not redundant
gff2.cpp:25:35: note: Null pointer addition
gff2.cpp:39:38: warning: Either the condition '0==ptrBandClust' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
gff2.cpp:36:8: note: Assuming that condition '0==ptrBandClust' is not redundant
gff2.cpp:39:38: note: Null pointer addition
gff2.cpp:51:27: warning: Either the condition '0==p' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
gff2.cpp:48:8: note: Assuming that condition '0==p' is not redundant
gff2.cpp:51:27: note: Null pointer addition
gff2.cpp:64:34: warning: Either the condition '0==ptrTarget' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
gff2.cpp:61:8: note: Assuming that condition '0==ptrTarget' is not redundant
gff2.cpp:64:34: note: Null pointer addition
gff2.cpp:68:31: warning: Either the condition '0==ptrBlank' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
gff2.cpp:66:8: note: Assuming that condition '0==ptrBlank' is not redundant
gff2.cpp:68:31: note: Null pointer subtraction
gff2.cpp:198:7: style: C-style pointer casting [cstyleCast]
gff2.cpp:199:7: style: C-style pointer casting [cstyleCast]
gff2.cpp:200:7: style: C-style pointer casting [cstyleCast]
gff2.cpp:201:7: style: C-style pointer casting [cstyleCast]
gff2.cpp:86:9: style: Variable 'End' can be declared as pointer to const [constVariablePointer]
gff2.cpp:114:9: style: Variable 'Ok' can be declared as pointer to const [constVariablePointer]
gff2.cpp:136:9: style: Variable 'SeqName' can be declared as pointer to const [constVariablePointer]
gff2.cpp:137:9: style: Variable 'Source' can be declared as pointer to const [constVariablePointer]
gff2.cpp:138:9: style: Variable 'Feature' can be declared as pointer to const [constVariablePointer]
gff2.cpp:139:9: style: Variable 'Start' can be declared as pointer to const [constVariablePointer]
gff2.cpp:140:9: style: Variable 'End' can be declared as pointer to const [constVariablePointer]
gff2.cpp:141:9: style: Variable 'Score' can be declared as pointer to const [constVariablePointer]
gff2.cpp:142:9: style: Variable 'Strand' can be declared as pointer to const [constVariablePointer]
gff2.cpp:143:9: style: Variable 'Frame' can be declared as pointer to const [constVariablePointer]
gff2.cpp:113:14: style: Variable 'TAB' is assigned a value that is never used. [unreadVariable]
gffset.cpp:67:3: style: C-style pointer casting [cstyleCast]
glix.cpp:50:12: style: The member function 'GLIX::Free' can be static. [functionStatic]
glix.h:21:7: note: The member function 'GLIX::Free' can be static.
glix.cpp:50:12: note: The member function 'GLIX::Free' can be static.
glix.cpp:207:9: warning: Either the condition '0==IE' is redundant or there is possible null pointer dereference: IE. [nullPointerRedundantCheck]
glix.cpp:205:8: note: Assuming that condition '0==IE' is not redundant
glix.cpp:207:9: note: Null pointer dereference
glix.cpp:215:9: warning: Either the condition '0==IE' is redundant or there is possible null pointer dereference: IE. [nullPointerRedundantCheck]
glix.cpp:213:8: note: Assuming that condition '0==IE' is not redundant
glix.cpp:215:9: note: Null pointer dereference
glix.cpp:258:16: warning: Either the condition '0==m_SeqMap' is redundant or there is possible null pointer dereference: m_SeqMap. [nullPointerRedundantCheck]
glix.cpp:254:8: note: Assuming that condition '0==m_SeqMap' is not redundant
glix.cpp:258:16: note: Null pointer dereference
glix.cpp:261:27: warning: Either the condition '0==IE' is redundant or there is possible null pointer dereference: IE. [nullPointerRedundantCheck]
glix.cpp:259:8: note: Assuming that condition '0==IE' is not redundant
glix.cpp:261:27: note: Null pointer dereference
glix.cpp:276:16: warning: Either the condition '0==m_SeqMap' is redundant or there is possible null pointer dereference: m_SeqMap. [nullPointerRedundantCheck]
glix.cpp:272:8: note: Assuming that condition '0==m_SeqMap' is not redundant
glix.cpp:276:16: note: Null pointer dereference
glix.cpp:279:27: warning: Either the condition '0==IE' is redundant or there is possible null pointer dereference: IE. [nullPointerRedundantCheck]
glix.cpp:277:8: note: Assuming that condition '0==IE' is not redundant
glix.cpp:279:27: note: Null pointer dereference
glix.cpp:61:16: style: C-style pointer casting [cstyleCast]
glix.cpp:80:15: style: C-style pointer casting [cstyleCast]
glix.cpp:132:15: style: C-style pointer casting [cstyleCast]
glix.cpp:224:13: style: C-style pointer casting [cstyleCast]
glix.cpp:109:39: style:inconclusive: Function 'Add' argument 2 names different: declaration 'LocalPos' definition 'Pos'. [funcArgNamesDifferent]
glix.h:33:34: note: Function 'Add' argument 2 names different: declaration 'LocalPos' definition 'Pos'.
glix.cpp:109:39: note: Function 'Add' argument 2 names different: declaration 'LocalPos' definition 'Pos'.
glix.cpp:231:13: style: Variable 'IE' can be declared as reference to const [constVariableReference]
glix.cpp:258:11: style: Variable 'IE' can be declared as pointer to const [constVariablePointer]
glix.cpp:276:11: style: Variable 'IE' can be declared as pointer to const [constVariablePointer]
glix.cpp:231:16: style: Variable 'IE' is assigned a value that is never used. [unreadVariable]
hash.cpp:78:20: style: C-style pointer casting [cstyleCast]
hash.cpp:123:20: style: C-style pointer casting [cstyleCast]
iix.cpp:104:19: warning: Either the condition '0==m_GLIX' is redundant or there is possible null pointer dereference: m_GLIX. [nullPointerRedundantCheck]
iix.cpp:101:8: note: Assuming that condition '0==m_GLIX' is not redundant
iix.cpp:104:19: note: Null pointer dereference
iix.cpp:64:13: style: C-style pointer casting [cstyleCast]
iix.cpp:88:18: style: C-style pointer casting [cstyleCast]
iix.cpp:129:6: style: C-style pointer casting [cstyleCast]
iix.cpp:122:18: style: Variable 'ii' can be declared as pointer to const [constVariablePointer]
log.cpp:20:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
log.cpp:45:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
log.cpp:37:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
log.cpp:51:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
main.cpp:82:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
makeannot.cpp:43:23: style: C-style pointer casting [cstyleCast]
makeannot.cpp:44:23: style: C-style pointer casting [cstyleCast]
makeannot.cpp:56:23: style: C-style pointer casting [cstyleCast]
makeannot.cpp:57:23: style: C-style pointer casting [cstyleCast]
makeannot.cpp:197:8: style: C-style pointer casting [cstyleCast]
makeannot.cpp:294:8: style: C-style pointer casting [cstyleCast]
makeannot.cpp:269:46: style:inconclusive: Function 'MakeAnnot' argument 2 names different: declaration 'Start' definition 'SeqFrom'. [funcArgNamesDifferent]
piler2.h:100:46: note: Function 'MakeAnnot' argument 2 names different: declaration 'Start' definition 'SeqFrom'.
makeannot.cpp:269:46: note: Function 'MakeAnnot' argument 2 names different: declaration 'Start' definition 'SeqFrom'.
makeannot.cpp:269:59: style:inconclusive: Function 'MakeAnnot' argument 3 names different: declaration 'End' definition 'SeqTo'. [funcArgNamesDifferent]
piler2.h:100:57: note: Function 'MakeAnnot' argument 3 names different: declaration 'End' definition 'SeqTo'.
makeannot.cpp:269:59: note: Function 'MakeAnnot' argument 3 names different: declaration 'End' definition 'SeqTo'.
makeannot.cpp:100:6: style: Local variable 'AnnotHitCount' shadows outer variable [shadowVariable]
makeannot.cpp:20:12: note: Shadowed declaration
makeannot.cpp:100:6: note: Shadow variable
makeannot.cpp:215:22: style: Variable 'RepContigFrom' is assigned a value that is never used. [unreadVariable]
makeannot.cpp:216:20: style: Variable 'RepContigTo' is assigned a value that is never used. [unreadVariable]
makeannot.cpp:317:11: style: Variable 'RepTo' is assigned a value that is never used. [unreadVariable]
mem.cpp:18:3: warning: If memory allocation fails, then there is a possible null pointer dereference: pSize [nullPointerOutOfMemory]
mem.cpp:14:27: note: Assuming allocation function fails
mem.cpp:14:12: note: Assignment 'p=(char*)std::malloc((unsigned long)(bytes+4))', assigned value is 0
mem.cpp:17:13: note: pSize is assigned '(int*)p' here.
mem.cpp:18:3: note: Null pointer dereference
mem.cpp:22:11: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
mem.cpp:14:27: note: Assuming allocation function fails
mem.cpp:14:12: note: Assignment 'p=(char*)std::malloc((unsigned long)(bytes+4))', assigned value is 0
mem.cpp:22:11: note: Null pointer addition
mem.cpp:14:12: style: C-style pointer casting [cstyleCast]
mem.cpp:29:24: style: C-style pointer casting [cstyleCast]
mem.cpp:33:8: style: C-style pointer casting [cstyleCast]
mem.cpp:48:24: style: C-style pointer casting [cstyleCast]
mem.cpp:17:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
mem.cpp:29:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
mem.cpp:48:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
mem.cpp:29:7: style: Variable 'pSize' can be declared as pointer to const [constVariablePointer]
mem.cpp:48:7: style: Variable 'pSize' can be declared as pointer to const [constVariablePointer]
options.cpp:78:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
options.cpp:146:9: style: Variable 'Value' can be declared as pointer to const [constVariablePointer]
options.cpp:80:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
progress.cpp:22:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
progress.cpp:40:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
progress.cpp:54:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
progress.cpp:66:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
progress.cpp:22:3: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
progress.cpp:22:3: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
progress.cpp:41:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
progress.cpp:67:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
quit.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
quit.cpp:38:2: error: va_list 'ArgList' was opened but not closed by va_end(). [va_end_missing]
readafa.cpp:20:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
readafa.cpp:8:17: style: C-style pointer casting [cstyleCast]
readhits.cpp:13:3: warning: Either the condition '0==Space' is redundant or there is possible null pointer dereference: Space. [nullPointerRedundantCheck]
readhits.cpp:11:8: note: Assuming that condition '0==Space' is not redundant
readhits.cpp:13:3: note: Null pointer dereference
readhits.cpp:20:3: warning: Either the condition '0==Space' is redundant or there is possible null pointer dereference: Space. [nullPointerRedundantCheck]
readhits.cpp:18:8: note: Assuming that condition '0==Space' is not redundant
readhits.cpp:20:3: note: Null pointer dereference
readhits.cpp:25:3: warning: Either the condition '0==Space' is redundant or there is possible null pointer dereference: Space. [nullPointerRedundantCheck]
readhits.cpp:23:8: note: Assuming that condition '0==Space' is not redundant
readhits.cpp:25:3: note: Null pointer dereference
readhits.cpp:21:22: warning: Either the condition '0==Space' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
readhits.cpp:18:8: note: Assuming that condition '0==Space' is not redundant
readhits.cpp:21:22: note: Null pointer addition
readhits.cpp:26:20: warning: Either the condition '0==Space' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
readhits.cpp:23:8: note: Assuming that condition '0==Space' is not redundant
readhits.cpp:26:20: note: Null pointer addition
readhits.cpp:114:18: style: C-style pointer casting [cstyleCast]
readhits.cpp:4:35: style: Parameter 'Rec' can be declared as reference to const [constParameterReference]
readhits.cpp:26:8: style: Variable 'End' can be declared as pointer to const [constVariablePointer]
readmfa.cpp:43:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
readmfa.cpp:29:17: style: C-style pointer casting [cstyleCast]
readmfa.cpp:60:5: style: C-style pointer casting [cstyleCast]
readmfa.cpp:33:6: style: Variable 'ContigFrom' is assigned a value that is never used. [unreadVariable]
readmotif.cpp:12:18: warning: Either the condition '0==Pyr' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
readmotif.cpp:7:8: note: Assuming that condition '0==Pyr' is not redundant
readmotif.cpp:12:18: note: Null pointer addition
readmotif.cpp:68:22: style: C-style pointer casting [cstyleCast]
readmotif.cpp:6:8: style: Variable 'Pyr' can be declared as pointer to const [constVariablePointer]
readreps.cpp:11:27: warning: Either the condition '0==Start' is redundant or there is possible null pointer dereference: Start. [nullPointerRedundantCheck]
readreps.cpp:8:8: note: Assuming that condition '0==Start' is not redundant
readreps.cpp:11:27: note: Null pointer dereference
readreps.cpp:17:15: warning: Either the condition '0==Space' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
readreps.cpp:15:8: note: Assuming that condition '0==Space' is not redundant
readreps.cpp:17:15: note: Null pointer addition
readreps.cpp:120:18: style: C-style pointer casting [cstyleCast]
readreps.cpp:32:14: style: The scope of the variable 'RepeatTo' can be reduced. [variableScope]
readreps.cpp:33:14: style: The scope of the variable 'RepeatLeft' can be reduced. [variableScope]
readtrs.cpp:13:3: warning: Either the condition '0==Space' is redundant or there is possible null pointer dereference: Space. [nullPointerRedundantCheck]
readtrs.cpp:11:8: note: Assuming that condition '0==Space' is not redundant
readtrs.cpp:13:3: note: Null pointer dereference
readtrs.cpp:88:18: style: C-style pointer casting [cstyleCast]
readtrs.cpp:61:12: style: Local variable 'TRS' shadows outer function [shadowFunction]
piler2.h:140:6: note: Shadowed declaration
readtrs.cpp:61:12: note: Shadow variable
readtrs.cpp:4:32: style: Parameter 'Rec' can be declared as reference to const [constParameterReference]
tan.cpp:45:22: style: C-style pointer casting [cstyleCast]
tan.cpp:457:15: style: C-style pointer casting [cstyleCast]
tan.cpp:187:39: warning: Either the condition '0==Count' is redundant or there is division by zero at line 187. [zerodivcond]
tan.cpp:184:8: note: Assuming that condition '0==Count' is not redundant
tan.cpp:187:39: note: Division by zero
tan.cpp:231:18: style: Local variable 'FamMember' shadows outer variable [shadowVariable]
tan.cpp:205:17: note: Shadowed declaration
tan.cpp:231:18: note: Shadow variable
tan.cpp:232:7: style: Local variable 'HitIndex' shadows outer variable [shadowVariable]
tan.cpp:206:6: note: Shadowed declaration
tan.cpp:232:7: note: Shadow variable
tan.cpp:235:18: style: Local variable 'Hit' shadows outer variable [shadowVariable]
tan.cpp:209:17: note: Shadowed declaration
tan.cpp:235:18: note: Shadow variable
tan.cpp:240:8: style: Local variable 's' shadows outer variable [shadowVariable]
tan.cpp:216:7: note: Shadowed declaration
tan.cpp:240:8: note: Shadow variable
tan.cpp:139:18: style: Variable 'FamMember1' can be declared as reference to const [constVariableReference]
tan.cpp:151:19: style: Variable 'FamMember2' can be declared as reference to const [constVariableReference]
tan.cpp:205:17: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
tan.cpp:231:18: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
tan.cpp:266:18: style: Variable 'FamMember1' can be declared as reference to const [constVariableReference]
tan.cpp:278:19: style: Variable 'FamMember2' can be declared as reference to const [constVariableReference]
tan.cpp:361:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
tanmotif2fasta.cpp:35:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
tanmotif2fasta.cpp:21:28: style: C-style pointer casting [cstyleCast]
tanmotif2fasta.cpp:22:28: style: C-style pointer casting [cstyleCast]
tanmotif2fasta.cpp:42:12: style: C-style pointer casting [cstyleCast]
tanmotif2fasta.cpp:87:8: style: C-style pointer casting [cstyleCast]
tanmotif2fasta.cpp:100:10: style: Variable 'FastaFileName' can be declared as pointer to const [constVariablePointer]
tr.cpp:102:11: style: C-style pointer casting [cstyleCast]
tr.cpp:174:17: style: C-style pointer casting [cstyleCast]
tr.cpp:102:9: style: Redundant assignment of 'Cands' to itself. [selfAssignment]
tr.cpp:203:71: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
tr.cpp:218:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
tr.cpp:209:13: style: Variable 'Rec.Strand' is assigned a value that is never used. [unreadVariable]
trs.cpp:20:33: style: C-style pointer casting [cstyleCast]
trs.cpp:82:18: style: C-style pointer casting [cstyleCast]
trs.cpp:83:18: style: C-style pointer casting [cstyleCast]
trs.cpp:89:26: style: C-style pointer casting [cstyleCast]
trs.cpp:90:26: style: C-style pointer casting [cstyleCast]
trs.cpp:121:10: style: C-style pointer casting [cstyleCast]
trs.cpp:159:17: style: C-style pointer casting [cstyleCast]
trs.cpp:365:30: style: C-style pointer casting [cstyleCast]
trs.cpp:366:22: style: C-style pointer casting [cstyleCast]
trs.cpp:419:18: style: C-style pointer casting [cstyleCast]
trs.cpp:470:22: style: C-style pointer casting [cstyleCast]
trs.cpp:506:22: style: C-style pointer casting [cstyleCast]
trs.cpp:507:22: style: C-style pointer casting [cstyleCast]
trs.cpp:609:19: style: C-style pointer casting [cstyleCast]
trs.cpp:401:11: style: Unsigned expression 'i' can't be negative so it is unnecessary to test it. [unsignedPositive]
trs.cpp:401:21: style: Unsigned expression 'j' can't be negative so it is unnecessary to test it. [unsignedPositive]
trs.cpp:486:8: style: Local variable 'FamIndex' shadows outer variable [shadowVariable]
trs.cpp:472:6: note: Shadowed declaration
trs.cpp:486:8: note: Shadow variable
trs.cpp:491:20: style: Local variable 'FamMember' shadows outer variable [shadowVariable]
trs.cpp:485:19: note: Shadowed declaration
trs.cpp:491:20: note: Shadow variable
trs.cpp:524:8: style: Local variable 'FamIndex' shadows outer variable [shadowVariable]
trs.cpp:509:6: note: Shadowed declaration
trs.cpp:524:8: note: Shadow variable
trs.cpp:531:11: style: Local variable 'FamIndex' shadows outer variable [shadowVariable]
trs.cpp:509:6: note: Shadowed declaration
trs.cpp:531:11: note: Shadow variable
trs.cpp:554:8: style: Local variable 'FamIndex' shadows outer variable [shadowVariable]
trs.cpp:509:6: note: Shadowed declaration
trs.cpp:554:8: note: Shadow variable
trs.cpp:560:20: style: Local variable 'FamMember' shadows outer variable [shadowVariable]
trs.cpp:553:19: note: Shadowed declaration
trs.cpp:560:20: note: Shadow variable
trs.cpp:600:6: style: Local variable 'SeqLength' shadows outer variable [shadowVariable]
trs.cpp:15:12: note: Shadowed declaration
trs.cpp:600:6: note: Shadow variable
trs.cpp:300:48: style: Parameter 'Pile' can be declared as reference to const [constParameterReference]
trs.cpp:381:40: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
trs.cpp:389:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
trs.cpp:411:40: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
trs.cpp:426:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
trs.cpp:467:45: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
trs.cpp:467:60: style: Parameter 'SuperFams' can be declared as reference to const [constParameterReference]
trs.cpp:482:12: style: Variable 'SFFams' can be declared as reference to const [constVariableReference]
trs.cpp:485:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
trs.cpp:491:20: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
trs.cpp:503:45: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
trs.cpp:520:12: style: Variable 'SFFams' can be declared as reference to const [constVariableReference]
trs.cpp:523:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
trs.cpp:550:12: style: Variable 'SFFams' can be declared as reference to const [constVariableReference]
trs.cpp:553:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
trs.cpp:560:20: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
trs.cpp:564:15: style: Variable 'Pile' can be declared as reference to const [constVariableReference]
trs.cpp:82:11: style: Variable 'Hit1' can be declared as pointer to const [constVariablePointer]
trs.cpp:83:11: style: Variable 'Hit2' can be declared as pointer to const [constVariablePointer]
trs.cpp:94:47: style: Parameter 'Images' can be declared as pointer to const [constParameterPointer]
trs.cpp:119:20: style: Parameter 'PileIndexes' can be declared as pointer to const [constParameterPointer]
trs.cpp:347:36: style: Parameter 'PartnersRev' can be declared as const array [constParameter]
trs.cpp:151:22: style: Variable 'TotalImageCount' is assigned a value that is never used. [unreadVariable]
trs.cpp:157:19: style: Variable 'TotalImageCount' is assigned a value that is never used. [unreadVariable]
trs.cpp:636:7: style: Variable 'Hits' is assigned a value that is never used. [unreadVariable]
trs.cpp:646:14: style: Variable 'PileIndexes' is assigned a value that is never used. [unreadVariable]
trs2fasta.cpp:23:24: style: C-style pointer casting [cstyleCast]
trs2fasta.cpp:24:24: style: C-style pointer casting [cstyleCast]
trs2fasta.cpp:46:12: style: C-style pointer casting [cstyleCast]
trs2fasta.cpp:115:8: style: C-style pointer casting [cstyleCast]
trs2fasta.cpp:9:18: style: Local variable 'TRS' shadows outer function [shadowFunction]
piler2.h:140:6: note: Shadowed declaration
trs2fasta.cpp:9:18: note: Shadow variable
trs2fasta.cpp:123:18: style: Local variable 'TRS' shadows outer function [shadowFunction]
piler2.h:140:6: note: Shadowed declaration
trs2fasta.cpp:123:18: note: Shadow variable
trs2fasta.cpp:128:10: style: Variable 'FastaFileName' can be declared as pointer to const [constVariablePointer]
usage.cpp:9:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
usage.cpp:20:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
utils.cpp:33:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
utils.cpp:41:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
utils.cpp:52:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
writecrisp.cpp:42:30: style:inconclusive: Function 'WriteArray' argument 2 names different: declaration 'ArrayIndex' definition 'FamIndex'. [funcArgNamesDifferent]
piler2.h:136:30: note: Function 'WriteArray' argument 2 names different: declaration 'ArrayIndex' definition 'FamIndex'.
writecrisp.cpp:42:30: note: Function 'WriteArray' argument 2 names different: declaration 'ArrayIndex' definition 'FamIndex'.
writeimages.cpp:40:30: style:inconclusive: Function 'WriteImages' argument 1 names different: declaration 'OutputFileName' definition 'FileName'. [funcArgNamesDifferent]
piler2.h:133:30: note: Function 'WriteImages' argument 1 names different: declaration 'OutputFileName' definition 'FileName'.
writeimages.cpp:40:30: note: Function 'WriteImages' argument 1 names different: declaration 'OutputFileName' definition 'FileName'.
writeimages.cpp:40:65: style:inconclusive: Function 'WriteImages' argument 3 names different: declaration 'PileCount' definition 'HitCount'. [funcArgNamesDifferent]
piler2.h:133:71: note: Function 'WriteImages' argument 3 names different: declaration 'PileCount' definition 'HitCount'.
writeimages.cpp:40:65: note: Function 'WriteImages' argument 3 names different: declaration 'PileCount' definition 'HitCount'.
writepiles.cpp:22:29: style:inconclusive: Function 'WritePiles' argument 1 names different: declaration 'OutputFileName' definition 'FileName'. [funcArgNamesDifferent]
piler2.h:132:29: note: Function 'WritePiles' argument 1 names different: declaration 'OutputFileName' definition 'FileName'.
writepiles.cpp:22:29: note: Function 'WritePiles' argument 1 names different: declaration 'OutputFileName' definition 'FileName'.
diff:
head crisp.cpp:188:20: style: Parameter 'PileIndexes' can be declared as pointer to const [constParameterPointer]
head crisp.cpp:371:40: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
head crisp.cpp:381:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
head trs.cpp:119:20: style: Parameter 'PileIndexes' can be declared as pointer to const [constParameterPointer]
head trs.cpp:381:40: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
head trs.cpp:389:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
head trs.cpp:467:45: style: Parameter 'Fams' can be declared as reference to const [constParameterReference]
head trs.cpp:467:60: style: Parameter 'SuperFams' can be declared as reference to const [constParameterReference]
head trs.cpp:482:12: style: Variable 'SFFams' can be declared as reference to const [constVariableReference]
head trs.cpp:485:19: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]
head trs.cpp:491:20: style: Variable 'FamMember' can be declared as reference to const [constVariableReference]


DONE