2023-03-19 01:05:42.687139
ftp://ftp.de.debian.org/debian/pool/main/k/kma/kma_1.4.11.orig.tar.xz
cppcheck-options: --library=posix --library=gnu  --showtime=top5 --check-library --inconclusive --enable=style,information --inline-suppr --disable=missingInclude --suppress=unmatchedSuppression --template=daca2 --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=valueFlowBailoutIncompleteVar -D__GNUC__ --platform=unix64 -j4
platform: Linux-5.19.0-35-generic-x86_64-with-glibc2.35
python: 3.10.6
client-version: 1.3.45
compiler: g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
cppcheck: head 2.10
head-info: 3b61ecd (2023-03-18 16:39:45 +0100)
count: 502 TO!
elapsed-time: 1727.5 1800.1
head-timing-info:
 Overall time: 0s

old-timing-info:

head results:
kma-1.4.11/chain.c:169:14: style: Condition 'gap=(points->qStart[j]-qEnd)' is always true [knownConditionTrueFalse]
kma-1.4.11/chain.c:137:12: note: Assuming that condition 'qEnd<points->qStart[j]' is not redundant
kma-1.4.11/chain.c:169:14: note: Condition 'gap=(points->qStart[j]-qEnd)' is always true
kma-1.4.11/chain.c:190:14: style: Condition 'gap=tGap' is always true [knownConditionTrueFalse]
kma-1.4.11/chain.c:186:13: note: Assuming that condition 'tEnd<tStart' is not redundant
kma-1.4.11/chain.c:187:20: note: Assignment 'tGap=tStart-tEnd', assigned value is greater than 0
kma-1.4.11/chain.c:190:14: note: Condition 'gap=tGap' is always true
kma-1.4.11/chain.c:353:14: style: Condition 'gap=(points->qStart[j]-qEnd)' is always true [knownConditionTrueFalse]
kma-1.4.11/chain.c:320:12: note: Assuming that condition 'qEnd<points->qStart[j]' is not redundant
kma-1.4.11/chain.c:353:14: note: Condition 'gap=(points->qStart[j]-qEnd)' is always true
kma-1.4.11/chain.c:403:14: style: Condition 'gap=tGap' is always true [knownConditionTrueFalse]
kma-1.4.11/chain.c:399:13: note: Assuming that condition 'tEnd<tStart' is not redundant
kma-1.4.11/chain.c:400:20: note: Assignment 'tGap=tStart-tEnd', assigned value is greater than 0
kma-1.4.11/chain.c:403:14: note: Condition 'gap=tGap' is always true
kma-1.4.11/chain.c:123:41: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/chain.c:154:44: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/chain.c:235:41: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/chain.c:306:41: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/chain.c:338:44: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/chain.c:382:44: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/chain.c:469:41: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/compdna.c:69:14: style: Variable 'dest->size' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/compdna.c:65:13: note: dest->size is assigned
kma-1.4.11/compdna.c:69:14: note: dest->size is overwritten
kma-1.4.11/compdna.c:287:8: style: Variable 'i' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/compdna.c:284:4: note: i is assigned
kma-1.4.11/compdna.c:287:8: note: i is overwritten
kma-1.4.11/compdna.c:287:15: style: Variable 'j' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/compdna.c:285:4: note: j is assigned
kma-1.4.11/compdna.c:287:15: note: j is overwritten
kma-1.4.11/compdna.c:99:50: style: Parameter 'seq' can be declared as pointer to const [constParameter]
kma-1.4.11/compkmers.c:42:48: style: Parameter 'qseq' can be declared as pointer to const [constParameter]
kma-1.4.11/compress.c:212:13: warning:inconclusive: Either the condition 'node_t=next_t' is redundant or there is possible null pointer dereference: node_t. [nullPointerRedundantCheck]
kma-1.4.11/compress.c:327:15: note: Assuming that condition 'node_t=next_t' is not redundant
kma-1.4.11/compress.c:212:13: note: Null pointer dereference
kma-1.4.11/compress.c:215:44: warning:inconclusive: Either the condition 'node_t=next_t' is redundant or there is possible null pointer dereference: node_t. [nullPointerRedundantCheck]
kma-1.4.11/compress.c:327:15: note: Assuming that condition 'node_t=next_t' is not redundant
kma-1.4.11/compress.c:215:44: note: Null pointer dereference
kma-1.4.11/compress.c:218:42: warning:inconclusive: Either the condition 'node_t=next_t' is redundant or there is possible null pointer dereference: node_t. [nullPointerRedundantCheck]
kma-1.4.11/compress.c:327:15: note: Assuming that condition 'node_t=next_t' is not redundant
kma-1.4.11/compress.c:218:42: note: Null pointer dereference
kma-1.4.11/compress.c:110:9: style: Variable 'v_size' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/align.c:231:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:233:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:527:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:762:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:794:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:796:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:1009:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:1011:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/align.c:1011:7: style: Variable 'mask' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/align.c:1012:6: style: Variable 'key' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/db.c:68:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/db.c:69:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/db.c:70:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/decon.c:95:10: style: Variable 'shifter' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/decon.c:90:10: note: shifter is assigned
kma-1.4.11/decon.c:95:10: note: shifter is overwritten
kma-1.4.11/decon.c:90:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/decon.c:134:19: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/decon.c:135:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/alnfrags.c:74:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:176:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:236:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:399:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:409:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:454:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:487:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:518:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:577:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:735:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:745:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:789:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:822:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:853:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:910:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1033:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1043:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1083:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1208:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1269:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1433:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1443:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1508:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1548:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1581:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1646:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1810:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1820:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1886:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1926:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:1959:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:2021:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:2123:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:2140:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:2211:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:2284:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/alnfrags.c:142:14: style: Variable 'read_score' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/alnfrags.c:137:15: note: read_score is assigned
kma-1.4.11/alnfrags.c:142:14: note: read_score is overwritten
kma-1.4.11/alnfrags.c:1158:14: style: Variable 'read_score' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/alnfrags.c:1144:15: note: read_score is assigned
kma-1.4.11/alnfrags.c:1158:14: note: read_score is overwritten
kma-1.4.11/alnfrags.c:1158:14: style: Variable 'read_score' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/alnfrags.c:1151:16: note: read_score is assigned
kma-1.4.11/alnfrags.c:1158:14: note: read_score is overwritten
kma-1.4.11/alnfrags.c:42:55: style: Parameter 'matched_templates' can be declared as pointer to const [constParameter]
kma-1.4.11/alnfrags.c:1248:11: style: Variable 'bestHits' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/alnfrags.c:1625:11: style: Variable 'bestHits' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/alnfrags.c:2208:13: style: Variable 'read_score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/ef.c:41:7: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
kma-1.4.11/ef.c:67:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/ef.c:77:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/ef.c:116:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/ef.c:126:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 5) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 6) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 7) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 9) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 10) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 11) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 12) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 13) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 14) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:134:3: warning: %u in format string (no. 15) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/ef.c:48:82: style: Parameter 'seq' can be declared as pointer to const [constParameter]
kma-1.4.11/frags.c:76:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/hashmapcci.c:452:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/hashmapcci.c:459:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/hashmapcci.c:517:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/hashmapcci.c:541:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/hashmapcci.c:594:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/hashmapcci.c:488:8: style: Condition '0<size' is always true [knownConditionTrueFalse]
kma-1.4.11/hashmapcci.c:486:31: note: Assignment 'size=((src->len>>5)+1)*sizeof(unsigned long)', assigned value is greater than 7
kma-1.4.11/hashmapcci.c:488:8: note: Condition '0<size' is always true
kma-1.4.11/hashmapcci.c:527:13: style: Condition 'check<0' is always false [knownConditionTrueFalse]
kma-1.4.11/hashmapcci.c:525:33: note: Assignment 'check=((src->len>>5)+1)*sizeof(unsigned long)', assigned value is greater than 7
kma-1.4.11/hashmapcci.c:527:13: note: Condition 'check<0' is always false
kma-1.4.11/hashmapcci.c:497:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/hashmapcci.c:597:13: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/hashmapcci.c:243:7: style: Variable 'next' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashmapcci.c:270:2: style: Variable 'newchain' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashmapcci.c:453:10: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashmapindex.c:377:15: warning: Possible null pointer dereference: src [nullPointer]
kma-1.4.11/hashmapindex.c:365:30: note: Assignment 'src=0', assigned value is 0
kma-1.4.11/hashmapindex.c:377:15: note: Null pointer dereference
kma-1.4.11/hashmapindex.c:378:17: warning: Possible null pointer dereference: src [nullPointer]
kma-1.4.11/hashmapindex.c:365:30: note: Assignment 'src=0', assigned value is 0
kma-1.4.11/hashmapindex.c:378:17: note: Null pointer dereference
kma-1.4.11/hashmapindex.c:243:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/hashmapindex.c:316:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/dist.c:245:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:257:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:315:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:348:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:371:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:417:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:420:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:491:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:514:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:587:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:590:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/dist.c:548:22: style: Condition 'j_end==i' is always false [knownConditionTrueFalse]
kma-1.4.11/dist.c:547:11: note: j_end is assigned '(i<j+chunk)?i:(j+chunk)' here.
kma-1.4.11/dist.c:548:22: note: Condition 'j_end==i' is always false
kma-1.4.11/dist.c:551:22: style: Condition 'j_end==Dist->n' is always false [knownConditionTrueFalse]
kma-1.4.11/dist.c:550:11: note: j_end is assigned '(Dist->n<j+chunk)?Dist->n:(j+chunk)' here.
kma-1.4.11/dist.c:551:22: note: Condition 'j_end==Dist->n' is always false
kma-1.4.11/dist.c:84:9: error: Dereferencing 'dest' after it is deallocated / released [deallocuse]
kma-1.4.11/dist.c:114:8: error: Dereferencing 'dest' after it is deallocated / released [deallocuse]
kma-1.4.11/dist.c:115:8: error: Dereferencing 'dest' after it is deallocated / released [deallocuse]
kma-1.4.11/dist.c:145:9: error: Dereferencing 'dest' after it is deallocated / released [deallocuse]
kma-1.4.11/dist.c:146:9: error: Dereferencing 'dest' after it is deallocated / released [deallocuse]
kma-1.4.11/dist.c:673:9: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:673:9: note: Null pointer dereference
kma-1.4.11/dist.c:674:11: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:674:11: note: Null pointer dereference
kma-1.4.11/dist.c:675:15: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:675:15: note: Null pointer dereference
kma-1.4.11/dist.c:676:6: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:676:6: note: Null pointer dereference
kma-1.4.11/dist.c:677:11: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:677:11: note: Null pointer dereference
kma-1.4.11/dist.c:678:11: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:678:11: note: Null pointer dereference
kma-1.4.11/dist.c:679:13: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:679:13: note: Null pointer dereference
kma-1.4.11/dist.c:680:14: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:680:14: note: Null pointer dereference
kma-1.4.11/dist.c:681:7: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:681:7: note: Null pointer dereference
kma-1.4.11/dist.c:682:9: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:682:9: note: Null pointer dereference
kma-1.4.11/dist.c:683:18: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:847:13: note: Calling function 'threadDist', 1st argument 'thread' value is 0
kma-1.4.11/dist.c:663:23: note: Assignment 'thread=arg', assigned value is 0
kma-1.4.11/dist.c:683:18: note: Null pointer dereference
kma-1.4.11/dist.c:846:2: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:846:2: note: Null pointer dereference
kma-1.4.11/dist.c:850:18: warning: Possible null pointer dereference: thread [nullPointer]
kma-1.4.11/dist.c:819:11: note: Assignment 'thread=0', assigned value is 0
kma-1.4.11/dist.c:822:9: note: Assuming condition is false
kma-1.4.11/dist.c:850:18: note: Null pointer dereference
kma-1.4.11/dist.c:59:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/dist.c:767:12: style: Variable 'outfileM' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/dist.c:1008:12: style: Variable 'file_len' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashmapkma.c:196:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/hashmapkma.c:292:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/hashmapkma.c:474:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/hashmapkma.c:614:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/hashmapkma.c:444:12: style: Variable 'seekSize' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashmapkma.c:588:12: style: Variable 'seekSize' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashtable.c:327:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
kma-1.4.11/hashtable.c:73:11: style: Variable 'kmerNode' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashtable.c:144:11: style: Variable 'kmerNode' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashtable.c:147:13: style: Variable 'decon_node' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashtable.c:323:15: style: Variable 'deConTable' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/hashtable.c:327:14: style: Variable 'deConTable' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/assembly.c:330:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:337:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:355:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:357:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:370:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:457:8: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:585:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:644:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:649:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:838:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:845:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:909:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:911:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:925:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1021:8: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1047:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1108:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1114:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1334:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1432:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1464:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1480:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1575:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1583:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1601:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1610:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1635:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1639:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1702:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1707:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1714:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1750:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1752:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1765:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1781:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1816:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1819:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1825:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1935:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1995:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1998:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:2005:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:2022:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:2042:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/assembly.c:1259:21: style: Variable 'nextTemplate' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/assembly.c:1258:17: note: nextTemplate is assigned
kma-1.4.11/assembly.c:1259:21: note: nextTemplate is overwritten
kma-1.4.11/assembly.c:85:71: style: Parameter 'template_seq' can be declared as pointer to const [constParameter]
kma-1.4.11/assembly.c:1452:76: style: Parameter 'seq' can be declared as pointer to const [constParameter]
kma-1.4.11/assembly.c:635:6: warning: Expression '-8' has a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
kma-1.4.11/assembly.c:1098:6: warning: Expression '-8' has a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
kma-1.4.11/assembly.c:1305:5: warning: Expression '-8' has a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
kma-1.4.11/assembly.c:1985:6: warning: Expression '-8' has a negative value. That is converted to an unsigned value and used in an unsigned calculation. [signConversion]
kma-1.4.11/assembly.c:373:16: style: Variable 'read_score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/assembly.c:928:16: style: Variable 'read_score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/assembly.c:1828:16: style: Variable 'read_score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/conclave.c:114:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck]
kma-1.4.11/conclave.c:286:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck]
kma-1.4.11/conclave.c:451:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck]
kma-1.4.11/conclave.c:645:39: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck]
kma-1.4.11/conclave.c:815:38: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck]
kma-1.4.11/conclave.c:1009:39: style: Array index 'tmp_template' is used before limits check. [arrayIndexThenCheck]
kma-1.4.11/conclave.c:43:165: style: Parameter 'alignment_scores' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:43:226: style: Parameter 'template_lengths' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:43:198: style: Parameter 'uniq_alignment_scores' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:216:168: style: Parameter 'alignment_scores' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:216:229: style: Parameter 'template_lengths' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:216:201: style: Parameter 'uniq_alignment_scores' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:388:166: style: Parameter 'alignment_scores' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:388:227: style: Parameter 'template_lengths' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:752:169: style: Parameter 'alignment_scores' can be declared as pointer to const [constParameter]
kma-1.4.11/conclave.c:752:230: style: Parameter 'template_lengths' can be declared as pointer to const [constParameter]
kma-1.4.11/kmapipe.c:99:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:108:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:127:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:180:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:219:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:229:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:243:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:257:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/kmapipe.c:109:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck]
kma-1.4.11/kmapipe.c:110:7: note: Assuming that condition '!src' is not redundant
kma-1.4.11/kmapipe.c:109:33: note: Null pointer dereference
kma-1.4.11/kmapipe.c:119:8: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck]
kma-1.4.11/kmapipe.c:129:7: note: Assuming that condition '!src' is not redundant
kma-1.4.11/kmapipe.c:119:8: note: Null pointer dereference
kma-1.4.11/kmapipe.c:128:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck]
kma-1.4.11/kmapipe.c:129:7: note: Assuming that condition '!src' is not redundant
kma-1.4.11/kmapipe.c:128:33: note: Null pointer dereference
kma-1.4.11/kmapipe.c:230:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck]
kma-1.4.11/kmapipe.c:231:7: note: Assuming that condition '!src' is not redundant
kma-1.4.11/kmapipe.c:230:33: note: Null pointer dereference
kma-1.4.11/kmapipe.c:242:25: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck]
kma-1.4.11/kmapipe.c:260:7: note: Assuming that condition '!src' is not redundant
kma-1.4.11/kmapipe.c:242:25: note: Null pointer dereference
kma-1.4.11/kmapipe.c:258:8: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck]
kma-1.4.11/kmapipe.c:260:7: note: Assuming that condition '!src' is not redundant
kma-1.4.11/kmapipe.c:258:8: note: Null pointer dereference
kma-1.4.11/kmapipe.c:259:33: warning: Either the condition '!src' is redundant or there is possible null pointer dereference: src. [nullPointerRedundantCheck]
kma-1.4.11/kmapipe.c:260:7: note: Assuming that condition '!src' is not redundant
kma-1.4.11/kmapipe.c:259:33: note: Null pointer dereference
kma-1.4.11/kmerlink.c:45:52: style: Parameter 'node' can be declared as pointer to const [constParameter]
kma-1.4.11/kmeranker.c:77:11: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/kmeranker.c:508:14: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/kmeranker.c:509:13: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/kmeranker.c:502:34: style:inconclusive: Function 'chooseChain' argument 1 names different: declaration 'bestScore' definition 'best_score'. [funcArgNamesDifferent]
kma-1.4.11/kmeranker.h:57:34: note: Function 'chooseChain' argument 1 names different: declaration 'bestScore' definition 'best_score'.
kma-1.4.11/kmeranker.c:502:34: note: Function 'chooseChain' argument 1 names different: declaration 'bestScore' definition 'best_score'.
kma-1.4.11/kmeranker.c:502:63: style:inconclusive: Function 'chooseChain' argument 2 names different: declaration 'bestScore_r' definition 'best_score_r'. [funcArgNamesDifferent]
kma-1.4.11/kmeranker.h:57:62: note: Function 'chooseChain' argument 2 names different: declaration 'bestScore_r' definition 'best_score_r'.
kma-1.4.11/kmeranker.c:502:63: note: Function 'chooseChain' argument 2 names different: declaration 'bestScore_r' definition 'best_score_r'.
kma-1.4.11/kmers.c:76:4: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
kma-1.4.11/kmers.c:141:12: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kmers.c:143:18: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kmers.c:145:18: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kmers.c:146:16: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kmers.c:147:8: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kmers.c:148:17: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kmers.c:149:21: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/loadupdate.c:51:29: style: Argument 'buffSize=1048576' to function smalloc is always 1048576. It does not matter what value 'buffSize' has. [knownArgument]
kma-1.4.11/kmmap.c:63:33: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/main.c:55:13: style: Condition '--argc' is always true [knownConditionTrueFalse]
kma-1.4.11/nw.c:253:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw.c:230:8: note: E_ptr is assigned
kma-1.4.11/nw.c:253:8: note: E_ptr is overwritten
kma-1.4.11/nw.c:582:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw.c:559:8: note: E_ptr is assigned
kma-1.4.11/nw.c:582:8: note: E_ptr is overwritten
kma-1.4.11/nw.c:852:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw.c:830:8: note: E_ptr is assigned
kma-1.4.11/nw.c:852:8: note: E_ptr is overwritten
kma-1.4.11/nw.c:1147:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw.c:1125:8: note: E_ptr is assigned
kma-1.4.11/nw.c:1147:8: note: E_ptr is overwritten
kma-1.4.11/mt1.c:455:3: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kma-1.4.11/mt1.c:455:3: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/mt1.c:115:20: warning: Either the condition 'outputfilename' is redundant or there is possible null pointer dereference: outputfilename. [nullPointerRedundantCheck]
kma-1.4.11/mt1.c:122:5: note: Assuming that condition 'outputfilename' is not redundant
kma-1.4.11/mt1.c:115:20: note: Null pointer dereference
kma-1.4.11/pherror.c:59:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/pherror.c:58:20: style: Condition 'nmemb==0' is always true [knownConditionTrueFalse]
kma-1.4.11/pherror.c:55:9: note: Assuming that condition '0<(nmemb=read(fileno(stream),ptr,size))' is not redundant
kma-1.4.11/pherror.c:58:20: note: Condition 'nmemb==0' is always true
kma-1.4.11/pherror.c:58:35: style: Condition 'nmemb==-1' is always false [knownConditionTrueFalse]
kma-1.4.11/pherror.c:58:20: note: Assuming that condition 'nmemb==0' is not redundant
kma-1.4.11/pherror.c:58:35: note: Condition 'nmemb==-1' is always false
kma-1.4.11/qualcheck.c:311:14: style: Condition 'thisKlen>=MinKlen' is always true [knownConditionTrueFalse]
kma-1.4.11/qualcheck.c:285:14: note: Assuming that condition 'thisKlen<MinKlen' is not redundant
kma-1.4.11/qualcheck.c:311:14: note: Condition 'thisKlen>=MinKlen' is always true
kma-1.4.11/qualcheck.c:181:3: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/qualcheck.c:313:4: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/qualcheck.c:189:103: style: Parameter 'template_ulengths' can be declared as pointer to const [constParameter]
kma-1.4.11/qualcheck.c:39:19: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/qualcheck.c:99:19: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/qualcheck.c:100:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/qualcheck.c:210:19: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/qualcheck.c:211:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:223:7: note: e is assigned
kma-1.4.11/nw2p.c:257:7: note: e is overwritten
kma-1.4.11/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:226:7: note: e is assigned
kma-1.4.11/nw2p.c:257:7: note: e is overwritten
kma-1.4.11/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:236:8: note: e is assigned
kma-1.4.11/nw2p.c:257:7: note: e is overwritten
kma-1.4.11/nw2p.c:257:7: style: Variable 'e' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:246:8: note: e is assigned
kma-1.4.11/nw2p.c:257:7: note: e is overwritten
kma-1.4.11/nw2p.c:340:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:317:8: note: E_ptr is assigned
kma-1.4.11/nw2p.c:340:8: note: E_ptr is overwritten
kma-1.4.11/nw2p.c:704:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:681:8: note: E_ptr is assigned
kma-1.4.11/nw2p.c:704:8: note: E_ptr is overwritten
kma-1.4.11/nw2p.c:974:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:952:8: note: E_ptr is assigned
kma-1.4.11/nw2p.c:974:8: note: E_ptr is overwritten
kma-1.4.11/nw2p.c:1269:8: style: Variable 'E_ptr' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/nw2p.c:1247:8: note: E_ptr is assigned
kma-1.4.11/nw2p.c:1269:8: note: E_ptr is overwritten
kma-1.4.11/nw2p.c:267:8: style: Variable 'Q2' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/sam.c:197:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/index.c:404:5: error: Common realloc mistake: 'deconfiles' nulled but not freed upon failure [memleakOnRealloc]
kma-1.4.11/index.c:430:5: error: Common realloc mistake: 'deconfiles' nulled but not freed upon failure [memleakOnRealloc]
kma-1.4.11/index.c:514:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/index.c:531:22: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/index.c:102:12: style: Variable 'templates' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/seq2fasta.c:51:39: style: Parameter 'template_lengths' can be declared as pointer to const [constParameter]
kma-1.4.11/seq2fasta.c:101:42: style: Parameter 'template_lengths' can be declared as pointer to const [constParameter]
kma-1.4.11/seq2fasta.c:233:11: style: Variable 'file_len' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/seqparse.c:390:13: style: Variable 'src->bytes' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/seqparse.c:386:14: note: src->bytes is assigned
kma-1.4.11/seqparse.c:390:13: note: src->bytes is overwritten
kma-1.4.11/seqparse.c:527:13: style: Variable 'src->bytes' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/seqparse.c:523:14: note: src->bytes is assigned
kma-1.4.11/seqparse.c:527:13: note: src->bytes is overwritten
kma-1.4.11/seqparse.c:66:69: style: Parameter 'trans' can be declared as pointer to const [constParameter]
kma-1.4.11/seqparse.c:161:57: style: Parameter 'trans' can be declared as pointer to const [constParameter]
kma-1.4.11/seqparse.c:241:81: style: Parameter 'trans' can be declared as pointer to const [constParameter]
kma-1.4.11/seqparse.c:396:69: style: Parameter 'trans' can be declared as pointer to const [constParameter]
kma-1.4.11/shm.c:69:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/shm.c:191:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/sparse.c:362:4: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
kma-1.4.11/sparse.c:617:5: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/sparse.c:764:5: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/sparse.c:56:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 66. [shiftTooManyBits]
kma-1.4.11/sparse.c:66:5: note: Assuming that condition 'prefix_len' is not redundant
kma-1.4.11/sparse.c:56:29: note: Shift
kma-1.4.11/savekmers.c:176:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:2135:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:2410:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:2932:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:2936:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:2945:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3233:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3237:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3246:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3342:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3358:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3400:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3428:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3454:3: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3521:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3537:6: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3592:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3599:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3631:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3662:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3721:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3737:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:4751:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:5015:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:5712:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:5718:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:6430:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/savekmers.c:3747:12: style: Condition 'hitCounter' is always true [knownConditionTrueFalse]
kma-1.4.11/savekmers.c:5179:11: style: Condition 'last' is always true [knownConditionTrueFalse]
kma-1.4.11/savekmers.c:5295:11: style: Condition 'last' is always true [knownConditionTrueFalse]
kma-1.4.11/savekmers.c:6128:12: style: Condition 'last' is always true [knownConditionTrueFalse]
kma-1.4.11/savekmers.c:5919:5: warning: Possible null pointer dereference: Sizes [nullPointer]
kma-1.4.11/savekmers.c:5840:22: note: Assignment 'Sizes=0', assigned value is 0
kma-1.4.11/savekmers.c:5919:5: note: Null pointer dereference
kma-1.4.11/savekmers.c:6442:9: warning: Either the condition 'best_score' is redundant or there is possible null pointer dereference: best_score. [nullPointerRedundantCheck]
kma-1.4.11/savekmers.c:6376:8: note: Assuming that condition 'best_score' is not redundant
kma-1.4.11/savekmers.c:6442:9: note: Null pointer dereference
kma-1.4.11/savekmers.c:306:16: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:376:16: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:1311:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:1505:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:1755:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:1816:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:4431:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:4769:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:5055:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:5056:12: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:5868:15: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:5869:12: portability: Casting between signed int * and double * which have an incompatible binary data representation. [invalidPointerCast]
kma-1.4.11/savekmers.c:2024:7: style: Variable 'end' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/savekmers.c:1943:6: note: end is assigned
kma-1.4.11/savekmers.c:2024:7: note: end is overwritten
kma-1.4.11/savekmers.c:2406:6: style: Variable 'end' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/savekmers.c:2175:6: note: end is assigned
kma-1.4.11/savekmers.c:2406:6: note: end is overwritten
kma-1.4.11/savekmers.c:5368:5: style: Variable 'rc' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/savekmers.c:5242:5: note: rc is assigned
kma-1.4.11/savekmers.c:5368:5: note: rc is overwritten
kma-1.4.11/savekmers.c:3762:182: style:inconclusive: Function 'save_kmers_HMM' argument 9 names different: declaration 'header' definition 'headerOrg'. [funcArgNamesDifferent]
kma-1.4.11/savekmers.h:86:182: note: Function 'save_kmers_HMM' argument 9 names different: declaration 'header' definition 'headerOrg'.
kma-1.4.11/savekmers.c:3762:182: note: Function 'save_kmers_HMM' argument 9 names different: declaration 'header' definition 'headerOrg'.
kma-1.4.11/savekmers.c:535:50: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:592:53: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:1096:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:1153:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:2237:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:2294:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:2520:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:2577:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:2755:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:2812:52: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:5432:49: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:6249:48: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
kma-1.4.11/savekmers.c:1238:25: style: Parameter 'bestTemplates' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1238:45: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1259:119: style: Parameter 'regionScores' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1259:29: style: Parameter 'bestTemplates' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1259:49: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1367:22: style: Parameter 'bestTemplates' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1367:42: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1399:47: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1399:117: style: Parameter 'regionScores' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1498:118: style: Parameter 'regionScores' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1632:20: style: Parameter 'bestTemplates' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1632:40: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:1666:40: style: Parameter 'bestTemplates_r' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:4419:88: style: Parameter 'template_lengths' can be declared as pointer to const [constParameter]
kma-1.4.11/savekmers.c:837:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 861. [shiftTooManyBits]
kma-1.4.11/savekmers.c:861:5: note: Assuming that condition 'prefix_len' is not redundant
kma-1.4.11/savekmers.c:836:22: note: Assignment 'prefix_shifter=64-(prefix_len<<1)', assigned value is 64
kma-1.4.11/savekmers.c:837:29: note: Shift
kma-1.4.11/savekmers.c:1929:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 1944. [shiftTooManyBits]
kma-1.4.11/savekmers.c:1944:5: note: Assuming that condition 'prefix_len' is not redundant
kma-1.4.11/savekmers.c:1928:22: note: Assignment 'prefix_shifter=64-(prefix_len<<1)', assigned value is 64
kma-1.4.11/savekmers.c:1929:29: note: Shift
kma-1.4.11/savekmers.c:807:9: style: Variable 'reps' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:860:6: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:1035:6: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:2486:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:2721:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:2928:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3012:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3071:8: style: Variable 'reps' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3133:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3193:8: style: Variable 'reps' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3229:7: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3296:17: style: Variable 'hitCounter' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3906:8: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:3926:14: style: Variable 'bestScore' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:4143:11: style: Variable 'Ms' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:4159:11: style: Variable 'Ms' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5080:21: style: Variable 'DB_size' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5550:12: style: Variable 'ties_len' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5552:18: style: Variable 'best_score_len' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5554:20: style: Variable 'best_score_len_r' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5594:11: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5634:11: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5713:7: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5719:7: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:5891:21: style: Variable 'DB_size' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:6352:14: style: Variable 'hitCounter' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:6372:12: style: Variable 'ties_len' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:6380:10: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/savekmers.c:6431:6: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1115:5: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kma-1.4.11/runkma.c:1129:3: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kma-1.4.11/runkma.c:213:20: warning: Either the condition 'outputfilename' is redundant or there is possible null pointer dereference: outputfilename. [nullPointerRedundantCheck]
kma-1.4.11/runkma.c:223:5: note: Assuming that condition 'outputfilename' is not redundant
kma-1.4.11/runkma.c:213:20: note: Null pointer dereference
kma-1.4.11/runkma.c:959:20: warning: Either the condition 'outputfilename' is redundant or there is possible null pointer dereference: outputfilename. [nullPointerRedundantCheck]
kma-1.4.11/runkma.c:975:5: note: Assuming that condition 'outputfilename' is not redundant
kma-1.4.11/runkma.c:959:20: note: Null pointer dereference
kma-1.4.11/stdnuc.c:278:38: style: Parameter 'compressor' can be declared as pointer to const [constParameter]
kma-1.4.11/stdnuc.c:287:48: style: Parameter 'Pos' can be declared as pointer to const [constParameter]
kma-1.4.11/stdnuc.c:312:58: style: Parameter 'kmersize' can be declared as pointer to const [constParameter]
kma-1.4.11/stdnuc.c:336:59: style: Parameter 'kmersize' can be declared as pointer to const [constParameter]
kma-1.4.11/stdnuc.c:453:23: style: Variable 'comp' can be declared as const array [constVariable]
kma-1.4.11/stdnuc.c:468:46: style: Parameter 'trans' can be declared as pointer to const [constParameter]
kma-1.4.11/runkma.c:1056:8: style: Variable 't_len' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1057:13: style: Variable 'read_score' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1147:11: style: Variable 'header_r' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1154:9: style: Variable 'qseq_r' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1413:8: style: Variable 'depth' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1414:7: style: Variable 'q_id' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1415:8: style: Variable 'cover' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/runkma.c:1416:10: style: Variable 'q_cover' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/tmp.c:36:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/tmp.c:69:6: style: Variable 'fd' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/tsv.c:46:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
kma-1.4.11/tsv.c:107:2: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
kma-1.4.11/tsv.c:86:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/tsv.c:89:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/tsv.c:46:2: style: Variable 'flag' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/tsv.c:107:2: style: Variable 'flag' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/update.c:96:21: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/update.c:97:12: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]
kma-1.4.11/updateindex.c:185:4: warning: Either the condition '!template_lengths' is redundant or there is possible null pointer dereference: template_lengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:6: note: Assuming that condition '!template_lengths' is not redundant
kma-1.4.11/updateindex.c:185:4: note: Null pointer dereference
kma-1.4.11/updateindex.c:186:24: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:49: note: Assuming that condition '!template_ulengths' is not redundant
kma-1.4.11/updateindex.c:186:24: note: Null pointer dereference
kma-1.4.11/updateindex.c:187:5: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:49: note: Assuming that condition '!template_ulengths' is not redundant
kma-1.4.11/updateindex.c:187:5: note: Null pointer dereference
kma-1.4.11/updateindex.c:188:4: warning: Either the condition '!template_slengths' is redundant or there is possible null pointer dereference: template_slengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:27: note: Assuming that condition '!template_slengths' is not redundant
kma-1.4.11/updateindex.c:188:4: note: Null pointer dereference
kma-1.4.11/updateindex.c:188:54: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:49: note: Assuming that condition '!template_ulengths' is not redundant
kma-1.4.11/updateindex.c:188:54: note: Null pointer dereference
kma-1.4.11/updateindex.c:189:4: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:49: note: Assuming that condition '!template_ulengths' is not redundant
kma-1.4.11/updateindex.c:189:4: note: Null pointer dereference
kma-1.4.11/updateindex.c:190:4: warning: Either the condition '!template_lengths' is redundant or there is possible null pointer dereference: template_lengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:6: note: Assuming that condition '!template_lengths' is not redundant
kma-1.4.11/updateindex.c:190:4: note: Null pointer dereference
kma-1.4.11/updateindex.c:190:52: warning: Either the condition '!template_ulengths' is redundant or there is possible null pointer dereference: template_ulengths. [nullPointerRedundantCheck]
kma-1.4.11/updateindex.c:191:49: note: Assuming that condition '!template_ulengths' is not redundant
kma-1.4.11/updateindex.c:190:52: note: Null pointer dereference
kma-1.4.11/updateindex.c:90:29: warning: Shifting 64-bit value by 64 bits is undefined behaviour. See condition at line 114. [shiftTooManyBits]
kma-1.4.11/updateindex.c:114:7: note: Assuming that condition 'prefix_len' is not redundant
kma-1.4.11/updateindex.c:89:17: note: prefix_shifter is assigned '64-(prefix_len<<1)' here.
kma-1.4.11/updateindex.c:90:29: note: Shift
kma-1.4.11/valueshash.c:60:35: style: Parameter 'values' can be declared as pointer to const [constParameter]
kma-1.4.11/valueshash.c:88:26: style: Parameter 'values' can be declared as pointer to const [constParameter]
kma-1.4.11/valueshash.c:98:25: style: Parameter 's1' can be declared as pointer to const [constParameter]
kma-1.4.11/valueshash.c:98:39: style: Parameter 's2' can be declared as pointer to const [constParameter]
kma-1.4.11/xml.c:103:16: portability: Undefined behaviour, pointer arithmetic 'counts-1' is out of bounds. [pointerOutOfBounds]
kma-1.4.11/xml.c:119:16: portability: Undefined behaviour, pointer arithmetic 'counts-1' is out of bounds. [pointerOutOfBounds]
kma-1.4.11/xml.c:200:2: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/xml.c:40:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/xml.c:136:2: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kma-1.4.11/xml.c:211:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
kma-1.4.11/xml.c:55:10: warning: Either the condition 'out' is redundant or there is possible null pointer dereference: out. [nullPointerRedundantCheck]
kma-1.4.11/xml.c:77:5: note: Assuming that condition 'out' is not redundant
kma-1.4.11/xml.c:76:9: note: Calling function 'capXML', 1st argument 'out' value is 0
kma-1.4.11/xml.c:55:10: note: Null pointer dereference
kma-1.4.11/xml.c:56:10: warning: Either the condition 'out' is redundant or there is possible null pointer dereference: out. [nullPointerRedundantCheck]
kma-1.4.11/xml.c:77:5: note: Assuming that condition 'out' is not redundant
kma-1.4.11/xml.c:76:9: note: Calling function 'capXML', 1st argument 'out' value is 0
kma-1.4.11/xml.c:56:10: note: Null pointer dereference
kma-1.4.11/xml.c:154:11: style: Variable 'bases' can be declared as const array [constVariable]
kma-1.4.11/vcf.c:143:35: error: Array 'assembly[pos].counts[6]' accessed at index 8, which is out of bounds. [arrayIndexOutOfBounds]
kma-1.4.11/vcf.c:138:10: note: Assignment 'nuc='-'', assigned value is 45
kma-1.4.11/vcf.c:142:20: note: Assignment 'bestNuc=nuc2num[nuc]', assigned value is 8
kma-1.4.11/vcf.c:143:35: note: Array index out of bounds
kma-1.4.11/vcf.c:153:18: error: Array 'bases[6]' accessed at index 8, which is out of bounds. [arrayIndexOutOfBounds]
kma-1.4.11/vcf.c:138:10: note: Assignment 'nuc='-'', assigned value is 45
kma-1.4.11/vcf.c:142:20: note: Assignment 'bestNuc=nuc2num[nuc]', assigned value is 8
kma-1.4.11/vcf.c:146:17: note: Assuming condition is false
kma-1.4.11/vcf.c:153:18: note: Array index out of bounds
kma-1.4.11/vcf.c:187:29: warning: Either the condition 'bestNuc=='-'' is redundant or the array 'assembly[pos].counts[6]' is accessed at index 8, which is out of bounds. [arrayIndexOutOfBoundsCond]
kma-1.4.11/vcf.c:244:16: note: Assuming that condition 'bestNuc=='-'' is not redundant
kma-1.4.11/vcf.c:183:20: note: Assignment 'nucNum=nuc2num[bestNuc]', assigned value is 8
kma-1.4.11/vcf.c:187:29: note: Array index out of bounds
kma-1.4.11/vcf.c:145:9: style: Variable 'i' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/vcf.c:135:4: note: i is assigned
kma-1.4.11/vcf.c:145:9: note: i is overwritten
kma-1.4.11/vcf.c:152:10: style: Variable 'nucNum' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/vcf.c:157:11: style: Variable 'nucNum' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/vcf.c:169:12: style: Variable 'nucNum' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/spltdb.c:586:8: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
kma-1.4.11/spltdb.c:615:4: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
kma-1.4.11/spltdb.c:1071:5: style: Condition 'progress' is always false [knownConditionTrueFalse]
kma-1.4.11/spltdb.c:1069:13: note: Assignment 'progress=0', assigned value is 0
kma-1.4.11/spltdb.c:1071:5: note: Condition 'progress' is always false
kma-1.4.11/spltdb.c:713:5: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kma-1.4.11/spltdb.c:804:3: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kma-1.4.11/spltdb.c:809:3: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
kma-1.4.11/spltdb.c:613:5: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/spltdb.c:832:11: style: Variable 'header_r' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/spltdb.c:839:9: style: Variable 'qseq_r' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/spltdb.c:1064:8: style: Variable 'depth' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/spltdb.c:1065:7: style: Variable 'q_id' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/spltdb.c:1066:8: style: Variable 'cover' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/spltdb.c:1067:10: style: Variable 'q_cover' is assigned a value that is never used. [unreadVariable]
kma-1.4.11/kma.c:336:6: error: Common realloc mistake: 'templatefilenames' nulled but not freed upon failure [memleakOnRealloc]
kma-1.4.11/kma.c:346:6: error: Common realloc mistake: 'templatefilenames' nulled but not freed upon failure [memleakOnRealloc]
kma-1.4.11/kma.c:1163:11: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kma.c:1164:27: portability: Casting from double * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
kma-1.4.11/kma.c:1068:21: style: Variable 'significantBase' is reassigned a value before the old one has been used. [redundantAssignment]
kma-1.4.11/kma.c:1064:22: note: significantBase is assigned
kma-1.4.11/kma.c:1068:21: note: significantBase is overwritten
kma-1.4.11/kma.c:792:20: style: Opposite expression on both sides of '<'. [oppositeExpression]
kma-1.4.11/kma.c:802:20: style: Opposite expression on both sides of '<'. [oppositeExpression]
kma-1.4.11/kma.c:812:19: style: Opposite expression on both sides of '<'. [oppositeExpression]
kma-1.4.11/kma.c:823:20: style: Opposite expression on both sides of '<'. [oppositeExpression]
kma-1.4.11/kma.c:834:20: style: Opposite expression on both sides of '<'. [oppositeExpression]
kma-1.4.11/kma.c:855:11: style: Opposite expression on both sides of '<'. [oppositeExpression]
kma-1.4.11/kma.c:866:11: style: Opposite expression on both sides of '<'. [oppositeExpression]
kma-1.4.11/kma.c:1407:46: warning:inconclusive: Multiplying sizeof() with sizeof() indicates a logic error. [multiplySizeof]

DONE