2025-05-10 16:35
ftp://ftp.de.debian.org/debian/pool/main/f/freebayes/freebayes_1.3.9.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-1022-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: beb3362 (2025-05-10 14:33:23 +0200)
count: 721 696
elapsed-time: 7.0 7.1
head-timing-info:

old-timing-info:

head results:
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:21:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable target_len [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:48:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable target_len [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:55:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable h [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:65:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:72:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable h [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:81:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n2i [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:143:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_targets [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:151:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable h [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:162:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable h [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:16:23: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamHeader.cpp:17:24: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:11:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mark_for_closure [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:44:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_region [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:52:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_bams [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:70:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_bams [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:110:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_region [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:124:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:151:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_cram_reference [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:179:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pool [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:187:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_hdr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:194:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fp [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:228:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_cram_reference [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:238:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mark_for_closure [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:365:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_region_idx [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:389:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:21:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:70:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_grv [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:89:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos2 [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:112:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos1 [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:122:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_sorted [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:179:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_sorted [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:243:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:321:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_sorted [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:356:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:400:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:422:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:467:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:478:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_sorted [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:484:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:495:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_sorted [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:502:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:620:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:680:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_sorted [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamReader.cpp:255:5: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:11:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hdr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:17:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:37:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fop [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:49:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fop [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:72:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fop [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:94:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_format [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:105:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fop [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:126:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pool [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamWriter.cpp:134:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fop [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:277:18: style: Condition 'i->pos2<inext->pos2' is always true [knownConditionTrueFalse]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:276:13: note: Assuming that condition 'i->pos2>=inext->pos2' is not redundant
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:277:18: note: Condition 'i->pos2<inext->pos2' is always true
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:37:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:41:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:45:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:52:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:56:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:68:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:86:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:97:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_cigar [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:154:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tid [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:221:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:237:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qname [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:245:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_data [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:304:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_data [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:329:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qseq [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:349:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qseq [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:378:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:420:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:445:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l_qseq [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:526:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:551:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:574:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:599:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tid [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:656:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:686:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:709:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_data [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:717:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:159:17: style: Unused variable: val [unusedVariable]
freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:215:17: style: Unused variable: val [unusedVariable]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:17:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos2 [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:23:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:56:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:69:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos1 [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:78:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:95:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:103:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:124:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos1 [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:166:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:182:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:209:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:215:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:224:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:254:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable strand [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:147:24: warning: Obsolete function 'alloca' called. [allocaCalled]
freebayes-1.3.9/contrib/SeqLib/src/GenomicRegion.cpp:147:17: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:32:10: style:inconclusive: Technically the member function 'SeqLib::free_delete::operator()' can be const. [functionConst]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:108:7: warning: If memory allocation fails, then there is a possible null pointer dereference: new_cig [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:106:42: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:106:25: note: Assignment 'new_cig=(uint32_t*)malloc(4*c.size())', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:108:7: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:119:12: warning: If memory allocation fails, then there is a possible null pointer dereference: oldd [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:119:12: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:126:21: warning: If memory allocation fails, then there is a possible null pointer dereference: oldd [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:126:21: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:129:39: warning: If memory allocation fails, then there is a possible null pointer dereference: new_cig [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:106:42: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:106:25: note: Assignment 'new_cig=(uint32_t*)malloc(4*c.size())', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:129:39: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:251:12: warning: If memory allocation fails, then there is a possible null pointer dereference: oldd [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:251:12: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:258:21: warning: If memory allocation fails, then there is a possible null pointer dereference: oldd [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:258:21: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:306:12: warning: If memory allocation fails, then there is a possible null pointer dereference: nonq [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:305:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:305:21: note: Assignment 'nonq=(uint8_t*)malloc(nonq_len)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:306:12: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:320:39: warning: If memory allocation fails, then there is a possible null pointer dereference: nonq [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:305:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:305:21: note: Assignment 'nonq=(uint8_t*)malloc(nonq_len)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:320:39: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:341:7: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:339:22: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:339:22: note: Assignment 'q=strdup(n.data())', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:341:7: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:342:29: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:339:22: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:339:22: note: Assignment 'q=strdup(n.data())', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:342:29: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:132:67: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:132:67: note: Null pointer addition
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:292:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:37: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:292:20: note: Null pointer addition
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:32:45: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:106:25: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:21: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:123:15: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:169:21: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:238:15: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:21: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:255:15: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:305:21: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:310:15: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:313:21: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:471:62: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:618:21: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:721:22: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:218:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable N [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:275:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:289:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translation_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:317:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translation_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:329:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translation_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:365:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translation_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:411:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_matrix_size_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:420:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translation_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:433:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translation_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:454:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:464:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw_cpp.cpp:471:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_matrix_ [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:100:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:158:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:352:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:399:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:584:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable s_align [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.cpp:312:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.cpp:334:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.cpp:425:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable scientific [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.cpp:1137:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.cpp:1294:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.cpp:1503:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.cpp:1516:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Allele.h:109:12: style:inconclusive: Member variable 'Allele::alternateSequence' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Allele.h:179:11: note: Member variable 'Allele::alternateSequence' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:109:12: note: Member variable 'Allele::alternateSequence' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:122:12: style:inconclusive: Member variable 'Allele::readGroupID' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Allele.h:182:11: note: Member variable 'Allele::readGroupID' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:122:12: note: Member variable 'Allele::readGroupID' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:110:12: style:inconclusive: Member variable 'Allele::sequencingTechnology' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Allele.h:183:11: note: Member variable 'Allele::sequencingTechnology' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:110:12: note: Member variable 'Allele::sequencingTechnology' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:130:12: style:inconclusive: Member variable 'Allele::readMismatchRate' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Allele.h:194:11: note: Member variable 'Allele::readMismatchRate' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:130:12: note: Member variable 'Allele::readMismatchRate' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:111:14: style:inconclusive: Member variable 'Allele::position' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Allele.h:225:11: note: Member variable 'Allele::position' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:111:14: note: Member variable 'Allele::position' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:130:12: style:inconclusive: Member variable 'Allele::readMismatchRate' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Allele.h:227:11: note: Member variable 'Allele::readMismatchRate' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:130:12: note: Member variable 'Allele::readMismatchRate' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:137:10: style:inconclusive: Member variable 'Allele::processed' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Allele.h:232:11: note: Member variable 'Allele::processed' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.h:137:10: note: Member variable 'Allele::processed' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Allele.cpp:462:14: style:inconclusive: Technically the member function 'Allele::equivalent' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:239:10: note: Technically the member function 'Allele::equivalent' can be const.
freebayes-1.3.9/src/Allele.cpp:462:14: note: Technically the member function 'Allele::equivalent' can be const.
freebayes-1.3.9/src/Allele.cpp:845:14: style:inconclusive: Technically the member function 'Allele::sameSample' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:257:10: note: Technically the member function 'Allele::sameSample' can be const.
freebayes-1.3.9/src/Allele.cpp:845:14: note: Technically the member function 'Allele::sameSample' can be const.
freebayes-1.3.9/src/Allele.cpp:1433:13: style:inconclusive: Technically the member function 'Allele::referenceLengthFromCigar' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:267:9: note: Technically the member function 'Allele::referenceLengthFromCigar' can be const.
freebayes-1.3.9/src/Allele.cpp:1433:13: note: Technically the member function 'Allele::referenceLengthFromCigar' can be const.
freebayes-1.3.9/src/Allele.cpp:1007:16: style:inconclusive: Technically the member function 'Allele::read3p' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:271:12: note: Technically the member function 'Allele::read3p' can be const.
freebayes-1.3.9/src/Allele.cpp:1007:16: note: Technically the member function 'Allele::read3p' can be const.
freebayes-1.3.9/src/Allele.cpp:1021:16: style:inconclusive: Technically the member function 'Allele::read5pNonNull' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:272:12: note: Technically the member function 'Allele::read5pNonNull' can be const.
freebayes-1.3.9/src/Allele.cpp:1021:16: note: Technically the member function 'Allele::read5pNonNull' can be const.
freebayes-1.3.9/src/Allele.cpp:1036:16: style:inconclusive: Technically the member function 'Allele::read3pNonNull' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:273:12: note: Technically the member function 'Allele::read3pNonNull' can be const.
freebayes-1.3.9/src/Allele.cpp:1036:16: note: Technically the member function 'Allele::read3pNonNull' can be const.
freebayes-1.3.9/src/Allele.cpp:1051:13: style:inconclusive: Technically the member function 'Allele::read5pNonNullBases' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:276:9: note: Technically the member function 'Allele::read5pNonNullBases' can be const.
freebayes-1.3.9/src/Allele.cpp:1051:13: note: Technically the member function 'Allele::read5pNonNullBases' can be const.
freebayes-1.3.9/src/Allele.cpp:1067:13: style:inconclusive: Technically the member function 'Allele::read3pNonNullBases' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:278:9: note: Technically the member function 'Allele::read3pNonNullBases' can be const.
freebayes-1.3.9/src/Allele.cpp:1067:13: note: Technically the member function 'Allele::read3pNonNullBases' can be const.
freebayes-1.3.9/src/Allele.cpp:18:13: style:inconclusive: Technically the member function 'Allele::bpLeft' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:311:9: note: Technically the member function 'Allele::bpLeft' can be const.
freebayes-1.3.9/src/Allele.cpp:18:13: note: Technically the member function 'Allele::bpLeft' can be const.
freebayes-1.3.9/src/Allele.cpp:22:13: style:inconclusive: Technically the member function 'Allele::bpRight' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:312:9: note: Technically the member function 'Allele::bpRight' can be const.
freebayes-1.3.9/src/Allele.cpp:22:13: note: Technically the member function 'Allele::bpRight' can be const.
freebayes-1.3.9/src/Allele.h:320:10: style:inconclusive: Technically the member function 'AllelePairIntCompare::operator()' can be const. [functionConst]
freebayes-1.3.9/src/Allele.h:327:10: style:inconclusive: Technically the member function 'AllelePositionCompare::operator()' can be const. [functionConst]
freebayes-1.3.9/src/Allele.cpp:105:9: style: Variable 'L' is assigned an expression that holds the same value. [redundantAssignment]
freebayes-1.3.9/src/Allele.cpp:63:11: note: L is assigned 'l' here.
freebayes-1.3.9/src/Allele.cpp:105:9: note: Variable 'L' is assigned an expression that holds the same value.
freebayes-1.3.9/src/Allele.cpp:640:17: style: The scope of the variable 'altbase' can be reduced. [variableScope]
freebayes-1.3.9/src/Allele.cpp:462:33: style:inconclusive: Function 'equivalent' argument 1 names different: declaration 'a' definition 'b'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Allele.h:239:29: note: Function 'equivalent' argument 1 names different: declaration 'a' definition 'b'.
freebayes-1.3.9/src/Allele.cpp:462:33: note: Function 'equivalent' argument 1 names different: declaration 'a' definition 'b'.
freebayes-1.3.9/src/Allele.cpp:682:70: style:inconclusive: Function 'groupAlleles' argument 1 names different: declaration 'alleles' definition 'sampleGroups'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Allele.h:376:70: note: Function 'groupAlleles' argument 1 names different: declaration 'alleles' definition 'sampleGroups'.
freebayes-1.3.9/src/Allele.cpp:682:70: note: Function 'groupAlleles' argument 1 names different: declaration 'alleles' definition 'sampleGroups'.
freebayes-1.3.9/src/Allele.cpp:901:65: style:inconclusive: Function 'genotypeAllele' argument 3 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Allele.h:385:70: note: Function 'genotypeAllele' argument 3 names different: declaration 'length' definition 'len'.
freebayes-1.3.9/src/Allele.cpp:901:65: note: Function 'genotypeAllele' argument 3 names different: declaration 'length' definition 'len'.
freebayes-1.3.9/src/Allele.cpp:901:114: style:inconclusive: Function 'genotypeAllele' argument 6 names different: declaration 'position' definition 'pos'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Allele.h:385:135: note: Function 'genotypeAllele' argument 6 names different: declaration 'position' definition 'pos'.
freebayes-1.3.9/src/Allele.cpp:901:114: note: Function 'genotypeAllele' argument 6 names different: declaration 'position' definition 'pos'.
freebayes-1.3.9/src/Allele.cpp:1090:37: style:inconclusive: Function 'subtract' argument 5 names different: declaration 'cigarstart' definition 'cigarStart'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Allele.h:290:41: note: Function 'subtract' argument 5 names different: declaration 'cigarstart' definition 'cigarStart'.
freebayes-1.3.9/src/Allele.cpp:1090:37: note: Function 'subtract' argument 5 names different: declaration 'cigarstart' definition 'cigarStart'.
freebayes-1.3.9/src/Allele.cpp:1091:37: style:inconclusive: Function 'subtract' argument 6 names different: declaration 'cigarend' definition 'cigarEnd'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Allele.h:291:41: note: Function 'subtract' argument 6 names different: declaration 'cigarend' definition 'cigarEnd'.
freebayes-1.3.9/src/Allele.cpp:1091:37: note: Function 'subtract' argument 6 names different: declaration 'cigarend' definition 'cigarEnd'.
freebayes-1.3.9/src/Allele.cpp:1454:40: style:inconclusive: Function 'mergeAllele' argument 1 names different: declaration 'allele' definition 'newAllele'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Allele.h:308:36: note: Function 'mergeAllele' argument 1 names different: declaration 'allele' definition 'newAllele'.
freebayes-1.3.9/src/Allele.cpp:1454:40: note: Function 'mergeAllele' argument 1 names different: declaration 'allele' definition 'newAllele'.
freebayes-1.3.9/src/Utility.h:131:43: performance: Function parameter 'source' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Utility.h:131:69: performance: Function parameter 'target' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Allele.cpp:901:47: performance: Function parameter 'alt' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Allele.cpp:901:77: performance: Function parameter 'cigar' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Allele.cpp:934:59: performance: Function parameter 'base' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Allele.cpp:945:48: performance: Function parameter 'base' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Allele.cpp:957:44: performance: Function parameter 'refbase' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Allele.cpp:957:60: performance: Function parameter 'altbase' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Allele.cpp:331:41: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:385:52: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:395:16: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:414:43: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:462:33: style: Parameter 'b' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:502:37: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:528:54: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:531:17: style: Variable 'thisAllele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:543:53: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:546:17: style: Variable 'thisAllele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:617:77: style: Parameter 'refseq' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:623:17: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:632:27: style: Variable 'group' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:640:17: style: Variable 'altbase' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:652:17: style: Variable 'altseq' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:654:17: style: Variable 'cigar' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:685:26: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:845:33: style: Parameter 'other' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:853:30: style: Parameter 'a' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:853:41: style: Parameter 'b' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:857:32: style: Parameter 'a' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:857:43: style: Parameter 'b' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:859:27: style: Parameter 'a' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:859:38: style: Parameter 'b' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:897:31: style: Parameter 'a' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:905:44: style: Parameter 'allowedEnumeratedTypes' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:934:43: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:945:32: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:957:28: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:1266:17: style: Parameter 'addToStart' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:1414:38: style: Parameter 'cigar' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:403:16: style: Variable 'allele' can be declared as pointer to const [constVariableReference]
freebayes-1.3.9/src/Allele.cpp:409:44: style: Parameter 'allele' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:503:13: style: Variable 'prev' can be declared as pointer to const [constVariablePointer]
freebayes-1.3.9/src/Allele.cpp:847:31: style: Parameter 'a' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:847:43: style: Parameter 'b' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:851:33: style: Parameter 'a' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:851:45: style: Parameter 'b' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/Allele.cpp:171:44: warning: Either the condition 'off>baseQualities.size()' is redundant or 'off' can have the value baseQualities.size(). Expression 'baseQualities.at(off)' causes access out of bounds. [containerOutOfBounds]
freebayes-1.3.9/src/Allele.cpp:168:36: note: Assuming that condition 'off>baseQualities.size()' is not redundant
freebayes-1.3.9/src/Allele.cpp:171:44: note: Access out of bounds
freebayes-1.3.9/src/Allele.cpp:505:32: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Allele.cpp:908:22: style: Consider using std::any_of, std::all_of, std::none_of, or std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Allele.cpp:928:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Allele.cpp:939:15: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Allele.cpp:950:15: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Allele.cpp:640:41: error: Out of bounds access in expression 'ordered.rbegin()' because 'ordered' is empty. [containerOutOfBounds]
freebayes-1.3.9/src/Allele.cpp:634:62: note: Assuming condition is false
freebayes-1.3.9/src/Allele.cpp:640:41: note: Access out of bounds
freebayes-1.3.9/src/Allele.cpp:916:22: style: Variable 'allowed' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/Allele.cpp:916:14: style: Variable 'allowed' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/Allele.cpp:333:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
freebayes-1.3.9/src/Genotype.h:61:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable currentBase [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:27:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:144:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:175:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:235:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:284:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:419:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:616:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:622:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:683:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:700:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:821:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:1004:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:1072:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:1264:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:1440:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:1984:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:2312:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:2364:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:2555:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:2638:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:2715:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:2783:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:2848:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:3002:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:3209:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:3230:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:3603:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:3626:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:3749:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:3853:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/BedReader.cpp:23:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/BedReader.h:52:5: style: Class 'BedReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
freebayes-1.3.9/src/BedReader.h:27:46: performance: Function parameter 'd' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/BedReader.h:57:27: style: Parameter 'fname' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/BedReader.cpp:49:42: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/BedReader.cpp:54:40: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Bias.cpp:9:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Bias.cpp:48:12: style:inconclusive: Technically the member function 'Bias::empty' can be const. [functionConst]
freebayes-1.3.9/src/Bias.h:25:10: note: Technically the member function 'Bias::empty' can be const.
freebayes-1.3.9/src/Bias.cpp:48:12: note: Technically the member function 'Bias::empty' can be const.
freebayes-1.3.9/src/Bias.cpp:18:13: style: Condition 'firstrecord' is always true [knownConditionTrueFalse]
freebayes-1.3.9/src/Bias.cpp:14:24: note: Assignment 'firstrecord=true', assigned value is 1
freebayes-1.3.9/src/Bias.cpp:18:13: note: Condition 'firstrecord' is always true
freebayes-1.3.9/src/Bias.cpp:4:25: style: Parameter 'file' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/CNV.cpp:5:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/CNV.cpp:4:12: style: The scope of the variable 'line' can be reduced. [variableScope]
freebayes-1.3.9/src/CNV.cpp:11:21: style: Local variable 'ploidy' shadows outer function [shadowFunction]
freebayes-1.3.9/src/CNV.h:26:9: note: Shadowed declaration
freebayes-1.3.9/src/CNV.cpp:11:21: note: Shadow variable
freebayes-1.3.9/src/CNV.cpp:19:21: style: Local variable 'ploidy' shadows outer function [shadowFunction]
freebayes-1.3.9/src/CNV.h:26:9: note: Shadowed declaration
freebayes-1.3.9/src/CNV.cpp:19:21: note: Shadow variable
freebayes-1.3.9/src/Contamination.cpp:9:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Contamination.cpp:4:34: style: Parameter 'file' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Contamination.cpp:14:9: style: Unused variable: last [unusedVariable]
freebayes-1.3.9/src/DataLikelihood.cpp:84:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/DataLikelihood.cpp:280:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable prob [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:576:4: error: Common realloc mistake: 'h_b' nulled but not freed upon failure [memleakOnRealloc]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:577:4: error: Common realloc mistake: 'e_b' nulled but not freed upon failure [memleakOnRealloc]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:578:4: error: Common realloc mistake: 'h_c' nulled but not freed upon failure [memleakOnRealloc]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:587:4: error: Common realloc mistake: 'direction' nulled but not freed upon failure [memleakOnRealloc]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:690:5: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:702:4: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:710:4: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:316:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:316:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:317:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:317:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:318:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:318:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:320:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:320:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:321:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:321:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:322:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:322:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:327:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:327:22: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:335:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:315:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:335:22: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:520:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:520:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:521:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:521:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:522:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:522:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:524:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:524:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:525:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:525:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:526:2: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:526:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:530:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:530:22: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:537:22: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:48: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:519:25: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:537:22: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:721:3: warning: If memory allocation fails, then there is a possible null pointer dereference: c1 [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:717:24: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:717:7: note: Assignment 'c1=(uint32_t*)malloc(l*sizeof(uint32_t))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:721:3: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:722:3: warning: If memory allocation fails, then there is a possible null pointer dereference: c1 [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:717:24: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:717:7: note: Assignment 'c1=(uint32_t*)malloc(l*sizeof(uint32_t))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:722:3: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:742:3: warning: If memory allocation fails, then there is a possible null pointer dereference: reverse [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:739:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:739:20: note: Assignment 'reverse=(int8_t*)calloc(end+1,sizeof(int8_t))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:742:3: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:743:3: warning: If memory allocation fails, then there is a possible null pointer dereference: reverse [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:739:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:739:20: note: Assignment 'reverse=(int8_t*)calloc(end+1,sizeof(int8_t))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:743:3: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:752:2: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:752:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:753:2: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:753:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:754:2: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:754:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:762:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:762:3: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:763:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:763:3: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:765:42: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:765:42: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:766:2: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:766:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:767:2: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:767:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:768:2: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:768:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:769:2: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:35: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:751:17: note: Assignment 'p=(s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:769:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:795:2: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:31: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:15: note: Assignment 'r=(s_align*)calloc(1,sizeof(s_align))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:795:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:796:2: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:31: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:15: note: Assignment 'r=(s_align*)calloc(1,sizeof(s_align))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:796:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:797:2: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:31: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:15: note: Assignment 'r=(s_align*)calloc(1,sizeof(s_align))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:797:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:798:2: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:31: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:794:15: note: Assignment 'r=(s_align*)calloc(1,sizeof(s_align))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:798:2: note: Null pointer dereference
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:213:27: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:34: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:213:27: note: Null pointer addition
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:229:24: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:34: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:229:24: note: Null pointer addition
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:444:27: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:34: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:444:27: note: Null pointer addition
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:456:24: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:34: note: Assuming allocation function fails
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:456:24: note: Null pointer addition
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:153:47: style: Variable 'end_read_column' is allocated memory that is never used. [unusedAllocatedMemory]
freebayes-1.3.9/contrib/SeqLib/src/ssw.c:394:47: style: Variable 'end_read_column' is allocated memory that is never used. [unusedAllocatedMemory]
freebayes-1.3.9/src/Genotype.h:184:5: warning: Member variable 'GenotypeCombo::priorProbGenotypesGivenHWE' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/NonCall.h:26:5: warning: Member variable 'NonCall::nCount' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/Genotype.h:117:15: style:inconclusive: Member variable 'SampleDataLikelihood::genotype' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Genotype.h:126:11: note: Member variable 'SampleDataLikelihood::genotype' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Genotype.h:117:15: note: Member variable 'SampleDataLikelihood::genotype' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Genotype.h:119:17: style:inconclusive: Member variable 'SampleDataLikelihood::marginal' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Genotype.h:129:11: note: Member variable 'SampleDataLikelihood::marginal' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Genotype.h:119:17: note: Member variable 'SampleDataLikelihood::marginal' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Genotype.h:173:17: style:inconclusive: Member variable 'GenotypeCombo::permutationsln' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/Genotype.h:191:11: note: Member variable 'GenotypeCombo::permutationsln' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Genotype.h:173:17: note: Member variable 'GenotypeCombo::permutationsln' is in the wrong place in the initializer list.
freebayes-1.3.9/src/AlleleParser.h:113:12: style:inconclusive: Member variable 'AllelicPrimitive::alt' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/AlleleParser.h:117:4: note: Member variable 'AllelicPrimitive::alt' is in the wrong place in the initializer list.
freebayes-1.3.9/src/AlleleParser.h:113:12: note: Member variable 'AllelicPrimitive::alt' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:34:9: style:inconclusive: Member variable 'NonCall::altCount' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/NonCall.h:20:11: note: Member variable 'NonCall::altCount' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:34:9: note: Member variable 'NonCall::altCount' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:35:9: style:inconclusive: Member variable 'NonCall::minDepth' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/NonCall.h:22:11: note: Member variable 'NonCall::minDepth' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:35:9: note: Member variable 'NonCall::minDepth' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:34:9: style:inconclusive: Member variable 'NonCall::altCount' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/NonCall.h:29:11: note: Member variable 'NonCall::altCount' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:34:9: note: Member variable 'NonCall::altCount' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:35:9: style:inconclusive: Member variable 'NonCall::minDepth' is in the wrong place in the initializer list. [initializerList]
freebayes-1.3.9/src/NonCall.h:31:11: note: Member variable 'NonCall::minDepth' is in the wrong place in the initializer list.
freebayes-1.3.9/src/NonCall.h:35:9: note: Member variable 'NonCall::minDepth' is in the wrong place in the initializer list.
freebayes-1.3.9/src/Genotype.h:56:9: performance: Variable 'alleles' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
freebayes-1.3.9/src/Genotype.h:253:10: style:inconclusive: Technically the member function 'GenotypeComboResultSorter::operator()' can be const. [functionConst]
freebayes-1.3.9/src/Genotype.h:264:10: style:inconclusive: Technically the member function 'GenotypeComboResultEqual::operator()' can be const. [functionConst]
freebayes-1.3.9/src/Genotype.h:271:10: style:inconclusive: Technically the member function 'SampleDataLikelihoodCompare::operator()' can be const. [functionConst]
freebayes-1.3.9/src/Genotype.h:278:10: style:inconclusive: Technically the member function 'SampleMarginalCompare::operator()' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:89:10: style:inconclusive: Technically the member function 'AlleleFilter::operator()' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:93:10: style:inconclusive: Technically the member function 'AlleleFilter::operator()' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:105:10: style:inconclusive: Technically the member function 'AllelePtrCmp::operator()' can be const. [functionConst]
freebayes-1.3.9/src/ResultData.h:21:10: style:inconclusive: Technically the member function 'DataLikelihoodCompare::operator()' can be const. [functionConst]
freebayes-1.3.9/src/Genotype.h:55:5: style: Class 'Genotype' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
freebayes-1.3.9/src/AlleleParser.h:62:5: style: Class 'RegisteredAlignment' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
freebayes-1.3.9/src/DataLikelihood.cpp:276:48: style: The scope of the variable 'invariantSampleDataLikelihoods' can be reduced. [variableScope]
freebayes-1.3.9/src/ResultData.h:38:57: style: Local variable 's' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/ResultData.h:33:46: note: Shadowed declaration
freebayes-1.3.9/src/ResultData.h:38:57: note: Shadow variable
freebayes-1.3.9/src/Genotype.h:55:30: style: Parameter 'ungroupedAlleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/AlleleParser.h:89:29: style: Parameter 'a' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/DataLikelihood.cpp:31:34: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/DataLikelihood.cpp:182:19: style: Variable 'genotype' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.h:93:30: style: Parameter 'a' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/AlleleParser.h:105:30: style: Parameter 'a' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/AlleleParser.h:105:42: style: Parameter 'b' can be declared as pointer to const [constParameterReference]
freebayes-1.3.9/src/Sum.h:10:16: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/DataLikelihood.cpp:35:34: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/DataLikelihood.cpp:39:34: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/DataLikelihood.cpp:51:41: error: Iterators of different containers 'emptyA' and 'emptyB' are used together. [mismatchingContainers]
freebayes-1.3.9/src/DataLikelihood.cpp:78:34: style: double result is assigned to long double variable. If the variable is long double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
freebayes-1.3.9/src/DataLikelihood.cpp:19:26: style: Variable 'observationCount' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/DataLikelihood.cpp:23:20: style: Variable 'countIn' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/DataLikelihood.cpp:73:35: style: Variable 'probi' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/DataLikelihood.cpp:19:9: style: Variable 'observationCount' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/DataLikelihood.cpp:23:12: style: Variable 'countIn' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/DataLikelihood.cpp:73:29: style: Variable 'probi' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/DataLikelihood.cpp:182:28: style: Variable 'genotype' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/Product.h:11:20: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/FBFasta.cpp:48:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:88:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:149:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:199:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:211:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:228:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:252:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:285:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/FBFasta.cpp:218:24: performance:inconclusive: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static. [functionStatic]
freebayes-1.3.9/src/FBFasta.h:59:16: note: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static.
freebayes-1.3.9/src/FBFasta.cpp:218:24: note: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static.
freebayes-1.3.9/src/FBFasta.cpp:283:28: style:inconclusive: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const. [functionConst]
freebayes-1.3.9/src/FBFasta.h:78:16: note: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const.
freebayes-1.3.9/src/FBFasta.cpp:283:28: note: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const.
freebayes-1.3.9/src/FBFasta.cpp:265:22: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:265:22: note: Null pointer dereference
freebayes-1.3.9/src/FBFasta.cpp:266:5: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:266:5: note: Null pointer dereference
freebayes-1.3.9/src/FBFasta.cpp:271:16: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:271:16: note: Null pointer dereference
freebayes-1.3.9/src/FBFasta.cpp:308:22: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:308:22: note: Null pointer dereference
freebayes-1.3.9/src/FBFasta.cpp:309:5: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:309:5: note: Null pointer dereference
freebayes-1.3.9/src/FBFasta.cpp:314:16: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:314:16: note: Null pointer dereference
freebayes-1.3.9/src/FBFasta.cpp:268:22: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:268:22: note: Null pointer addition
freebayes-1.3.9/src/FBFasta.cpp:311:22: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
freebayes-1.3.9/src/FBFasta.cpp:311:22: note: Null pointer addition
freebayes-1.3.9/src/FBFasta.cpp:263:17: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/src/FBFasta.cpp:306:17: style: C-style pointer casting [cstyleCast]
freebayes-1.3.9/src/FBFasta.cpp:46:12: style: The scope of the variable 'line' can be reduced. [variableScope]
freebayes-1.3.9/src/FBFasta.cpp:47:15: style: The scope of the variable 'linenum' can be reduced. [variableScope]
freebayes-1.3.9/src/FBFasta.cpp:103:9: style: The scope of the variable 'line_length' can be reduced. [variableScope]
freebayes-1.3.9/src/FBFasta.cpp:104:15: style: The scope of the variable 'offset' can be reduced. [variableScope]
freebayes-1.3.9/src/FBFasta.cpp:105:15: style: The scope of the variable 'line_number' can be reduced. [variableScope]
freebayes-1.3.9/src/FBFasta.cpp:106:10: style: The scope of the variable 'mismatchedLineLengths' can be reduced. [variableScope]
freebayes-1.3.9/src/FBFasta.cpp:111:10: style: The scope of the variable 'emptyLine' can be reduced. [variableScope]
freebayes-1.3.9/src/FBFasta.cpp:80:54: style:inconclusive: Function 'operator<<' argument 2 names different: declaration 'i' definition 'fastaIndex'. [funcArgNamesDifferent]
freebayes-1.3.9/src/FBFasta.h:62:50: note: Function 'operator<<' argument 2 names different: declaration 'i' definition 'fastaIndex'.
freebayes-1.3.9/src/FBFasta.cpp:80:54: note: Function 'operator<<' argument 2 names different: declaration 'i' definition 'fastaIndex'.
freebayes-1.3.9/src/FBFasta.cpp:93:44: style:inconclusive: Function 'indexReference' argument 1 names different: declaration 'refName' definition 'refname'. [funcArgNamesDifferent]
freebayes-1.3.9/src/FBFasta.h:53:36: note: Function 'indexReference' argument 1 names different: declaration 'refName' definition 'refname'.
freebayes-1.3.9/src/FBFasta.cpp:93:44: note: Function 'indexReference' argument 1 names different: declaration 'refName' definition 'refname'.
freebayes-1.3.9/src/FBFasta.cpp:208:50: style:inconclusive: Function 'entry' argument 1 names different: declaration 'key' definition 'name'. [funcArgNamesDifferent]
freebayes-1.3.9/src/FBFasta.h:57:38: note: Function 'entry' argument 1 names different: declaration 'key' definition 'name'.
freebayes-1.3.9/src/FBFasta.cpp:208:50: note: Function 'entry' argument 1 names different: declaration 'key' definition 'name'.
freebayes-1.3.9/src/FBFasta.cpp:101:21: style: Local variable 'entry' shadows outer function [shadowFunction]
freebayes-1.3.9/src/FBFasta.h:57:25: note: Shadowed declaration
freebayes-1.3.9/src/FBFasta.cpp:101:21: note: Shadow variable
freebayes-1.3.9/src/FBFasta.cpp:45:43: performance: Function parameter 'fname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:78:51: performance: Function parameter 'a' should be passed by const reference. However it seems that 'fastaIndexEntryCompare' is a callback function. [passedByValueCallback]
freebayes-1.3.9/src/FBFasta.cpp:86:50: note: Function pointer used here.
freebayes-1.3.9/src/FBFasta.cpp:78:51: note: Function parameter 'a' should be passed by const reference. However it seems that 'fastaIndexEntryCompare' is a callback function.
freebayes-1.3.9/src/FBFasta.cpp:78:74: performance: Function parameter 'b' should be passed by const reference. However it seems that 'fastaIndexEntryCompare' is a callback function. [passedByValueCallback]
freebayes-1.3.9/src/FBFasta.cpp:86:50: note: Function pointer used here.
freebayes-1.3.9/src/FBFasta.cpp:78:74: note: Function parameter 'b' should be passed by const reference. However it seems that 'fastaIndexEntryCompare' is a callback function.
freebayes-1.3.9/src/FBFasta.cpp:93:44: performance: Function parameter 'refname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:192:44: performance: Function parameter 'fname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:225:38: performance: Function parameter 'reffilename' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:259:50: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:277:47: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:283:60: performance: Function parameter 'seqnameStart' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:292:53: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:320:50: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:325:61: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/FBFasta.cpp:103:21: style: Variable 'line_length' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/FBFasta.cpp:265:14: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/FBFasta.cpp:265:12: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/FBFasta.cpp:308:14: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/FBFasta.cpp:308:12: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/IndelAllele.cpp:15:27: performance: Function parameter 'sequence' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Genotype.cpp:318:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Genotype.cpp:325:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Genotype.cpp:1306:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable allele [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Genotype.cpp:1645:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/LeftAlign.cpp:271:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Genotype.cpp:693:21: style:inconclusive: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const. [functionConst]
freebayes-1.3.9/src/Genotype.h:218:10: note: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const.
freebayes-1.3.9/src/Genotype.cpp:693:21: note: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const.
freebayes-1.3.9/src/Genotype.cpp:1054:40: style: The scope of the variable 'oldsdl_ptr' can be reduced. [variableScope]
freebayes-1.3.9/src/Genotype.cpp:30:51: style:inconclusive: Function 'alternateAlleles' argument 1 names different: declaration 'refbase' definition 'base'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:81:45: note: Function 'alternateAlleles' argument 1 names different: declaration 'refbase' definition 'base'.
freebayes-1.3.9/src/Genotype.cpp:30:51: note: Function 'alternateAlleles' argument 1 names different: declaration 'refbase' definition 'base'.
freebayes-1.3.9/src/Genotype.cpp:40:49: style:inconclusive: Function 'alternateBases' argument 1 names different: declaration 'refbase' definition 'base'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:82:43: note: Function 'alternateBases' argument 1 names different: declaration 'refbase' definition 'base'.
freebayes-1.3.9/src/Genotype.cpp:40:49: note: Function 'alternateBases' argument 1 names different: declaration 'refbase' definition 'base'.
freebayes-1.3.9/src/Genotype.cpp:95:68: style:inconclusive: Function 'relativeGenotype' argument 2 names different: declaration 'altbases' definition 'alts'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:90:62: note: Function 'relativeGenotype' argument 2 names different: declaration 'altbases' definition 'alts'.
freebayes-1.3.9/src/Genotype.cpp:95:68: note: Function 'relativeGenotype' argument 2 names different: declaration 'altbases' definition 'alts'.
freebayes-1.3.9/src/Genotype.cpp:126:46: style:inconclusive: Function 'relativeGenotype' argument 1 names different: declaration 'spec' definition 'rg'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:91:40: note: Function 'relativeGenotype' argument 1 names different: declaration 'spec' definition 'rg'.
freebayes-1.3.9/src/Genotype.cpp:126:46: note: Function 'relativeGenotype' argument 1 names different: declaration 'spec' definition 'rg'.
freebayes-1.3.9/src/Genotype.cpp:126:83: style:inconclusive: Function 'relativeGenotype' argument 3 names different: declaration 'altbases' definition 'alts'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:91:79: note: Function 'relativeGenotype' argument 3 names different: declaration 'altbases' definition 'alts'.
freebayes-1.3.9/src/Genotype.cpp:126:83: note: Function 'relativeGenotype' argument 3 names different: declaration 'altbases' definition 'alts'.
freebayes-1.3.9/src/Genotype.cpp:268:24: style:inconclusive: Function 'IUPAC' argument 1 names different: declaration 'g' definition 'genotype'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:109:24: note: Function 'IUPAC' argument 1 names different: declaration 'g' definition 'genotype'.
freebayes-1.3.9/src/Genotype.cpp:268:24: note: Function 'IUPAC' argument 1 names different: declaration 'g' definition 'genotype'.
freebayes-1.3.9/src/Genotype.cpp:316:56: style:inconclusive: Function 'operator<<' argument 2 names different: declaration 'combo' definition 'g'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:444:56: note: Function 'operator<<' argument 2 names different: declaration 'combo' definition 'g'.
freebayes-1.3.9/src/Genotype.cpp:316:56: note: Function 'operator<<' argument 2 names different: declaration 'combo' definition 'g'.
freebayes-1.3.9/src/Genotype.cpp:1106:28: style:inconclusive: Function 'convergentGenotypeComboSearch' argument 4 names different: declaration 'variantDataLikelihoods' definition 'variantSampleDataLikelihoods'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:404:28: note: Function 'convergentGenotypeComboSearch' argument 4 names different: declaration 'variantDataLikelihoods' definition 'variantSampleDataLikelihoods'.
freebayes-1.3.9/src/Genotype.cpp:1106:28: note: Function 'convergentGenotypeComboSearch' argument 4 names different: declaration 'variantDataLikelihoods' definition 'variantSampleDataLikelihoods'.
freebayes-1.3.9/src/Genotype.cpp:1107:28: style:inconclusive: Function 'convergentGenotypeComboSearch' argument 5 names different: declaration 'invariantDataLikelihoods' definition 'invariantSampleDataLikelihoods'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:405:28: note: Function 'convergentGenotypeComboSearch' argument 5 names different: declaration 'invariantDataLikelihoods' definition 'invariantSampleDataLikelihoods'.
freebayes-1.3.9/src/Genotype.cpp:1107:28: note: Function 'convergentGenotypeComboSearch' argument 5 names different: declaration 'invariantDataLikelihoods' definition 'invariantSampleDataLikelihoods'.
freebayes-1.3.9/src/Genotype.cpp:1505:14: style:inconclusive: Function 'calculatePosteriorProbability' argument 6 names different: declaration 'obsBinomialPriors' definition 'binomialObsPriors'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:240:14: note: Function 'calculatePosteriorProbability' argument 6 names different: declaration 'obsBinomialPriors' definition 'binomialObsPriors'.
freebayes-1.3.9/src/Genotype.cpp:1505:14: note: Function 'calculatePosteriorProbability' argument 6 names different: declaration 'obsBinomialPriors' definition 'binomialObsPriors'.
freebayes-1.3.9/src/Genotype.cpp:1507:21: style:inconclusive: Function 'calculatePosteriorProbability' argument 8 names different: declaration 'diffusionPriorScalarln' definition 'diffusionPriorScalar'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Genotype.h:242:21: note: Function 'calculatePosteriorProbability' argument 8 names different: declaration 'diffusionPriorScalarln' definition 'diffusionPriorScalar'.
freebayes-1.3.9/src/Genotype.cpp:1507:21: note: Function 'calculatePosteriorProbability' argument 8 names different: declaration 'diffusionPriorScalarln' definition 'diffusionPriorScalar'.
freebayes-1.3.9/src/Genotype.cpp:31:20: style: Local variable 'alleles' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/Genotype.h:50:20: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:31:20: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:41:20: style: Local variable 'alleles' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/Genotype.h:50:20: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:41:20: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:394:37: style: Local variable 'alleles' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:217:20: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:394:37: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:507:40: style: Local variable 'alleles' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:217:20: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:507:40: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:557:40: style: Local variable 'alleles' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:217:20: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:557:40: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:647:17: style: Local variable 'counts' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:214:17: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:647:17: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:1419:9: style: Local variable 'ploidy' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:204:9: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:1419:9: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:1696:17: style: Local variable 'counts' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:83:17: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:1696:17: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:1724:17: style: Local variable 'counts' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:83:17: note: Shadowed declaration
freebayes-1.3.9/src/Genotype.cpp:1724:17: note: Shadow variable
freebayes-1.3.9/src/Genotype.cpp:289:33: performance: Function parameter 'iupac' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Genotype.cpp:1608:98: performance: Function parameter 'altbase' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Genotype.cpp:30:51: style: Parameter 'base' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:33:17: style: Variable 'b' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Genotype.cpp:40:49: style: Parameter 'base' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:43:17: style: Variable 'b' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Genotype.cpp:95:43: style: Parameter 'refbase' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:95:68: style: Parameter 'alts' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:99:17: style: Variable 'base' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Genotype.cpp:126:58: style: Parameter 'refbase' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:126:83: style: Parameter 'alts' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:129:17: style: Variable 'base' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Genotype.cpp:154:66: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:157:17: style: Variable 'base' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Genotype.cpp:177:43: style: Parameter 'refbase' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:177:60: style: Parameter 'altbase' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:180:17: style: Variable 'b' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Genotype.cpp:268:24: style: Parameter 'genotype' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:316:56: style: Parameter 'g' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:1608:60: style: Parameter 'observations' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:1608:82: style: Parameter 'refbase' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:1734:63: style: Parameter 'ploidies' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Genotype.cpp:1882:28: style: Variable 'combo' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Genotype.cpp:1741:61: performance: Searching before insertion is not necessary. Instead of 'genotypesByPloidy[ploidy]=allPossibleGenotypes(ploidy,genotypeAlleles)' consider using 'genotypesByPloidy.try_emplace(ploidy, allPossibleGenotypes(ploidy,genotypeAlleles));'. [stlFindInsert]
freebayes-1.3.9/src/Genotype.cpp:1726:22: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Genotype.cpp:1793:30: style: Variable 'sample' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/LeftAlign.cpp:282:35: style: Condition 'indel.position>=lastend' is always true [knownConditionTrueFalse]
freebayes-1.3.9/src/LeftAlign.cpp:270:28: note: Assuming that condition 'indel.position<lastend' is not redundant
freebayes-1.3.9/src/LeftAlign.cpp:282:35: note: Condition 'indel.position>=lastend' is always true
freebayes-1.3.9/src/LeftAlign.cpp:114:17: style: Local variable 'steppos' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/LeftAlign.cpp:109:13: note: Shadowed declaration
freebayes-1.3.9/src/LeftAlign.cpp:114:17: note: Shadow variable
freebayes-1.3.9/src/LeftAlign.cpp:115:17: style: Local variable 'readsteppos' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/LeftAlign.cpp:109:22: note: Shadowed declaration
freebayes-1.3.9/src/LeftAlign.cpp:115:17: note: Shadow variable
freebayes-1.3.9/src/LeftAlign.cpp:344:49: performance: Function parameter 'referenceSequence' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/LeftAlign.cpp:187:28: style: Variable 'indel' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Marginals.cpp:72:39: style: Variable 'sdls' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Marginals.cpp:179:39: style: Variable 'sdls' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:883:15: warning: Member variable 'AlleleParser::fastaReferenceSequenceCount' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/AlleleParser.cpp:883:15: warning: Member variable 'AlleleParser::hasTarget' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/AlleleParser.cpp:883:15: warning: Member variable 'AlleleParser::currentReferenceBase' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/AlleleParser.cpp:883:15: warning: Member variable 'AlleleParser::currentAlternateAllele' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/AlleleParser.cpp:883:15: warning: Member variable 'AlleleParser::hasMoreVariants' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/AlleleParser.cpp:883:15: warning: Member variable 'AlleleParser::basesBeforeCurrentTarget' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/AlleleParser.cpp:883:15: warning: Member variable 'AlleleParser::basesAfterCurrentTarget' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/AlleleParser.cpp:2542:20: style:inconclusive: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:250:10: note: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:2542:20: note: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:2562:20: style:inconclusive: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:251:10: note: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:2562:20: note: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:2606:20: performance:inconclusive: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace). [functionStatic]
freebayes-1.3.9/src/AlleleParser.h:254:10: note: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:2606:20: note: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:2617:20: performance:inconclusive: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace). [functionStatic]
freebayes-1.3.9/src/AlleleParser.h:255:10: note: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:2617:20: note: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:2596:20: style:inconclusive: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:257:10: note: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:2596:20: note: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:942:19: style:inconclusive: Technically the member function 'AlleleParser::currentSequencePosition' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:273:9: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:942:19: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:947:19: style:inconclusive: Technically the member function 'AlleleParser::currentSequencePosition' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:274:9: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:947:19: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:4083:19: style:inconclusive: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:294:9: note: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:4083:19: note: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:4097:19: style:inconclusive: Technically the member function 'AlleleParser::homopolymerRunRight' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:295:9: note: Technically the member function 'AlleleParser::homopolymerRunRight' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:4097:19: note: Technically the member function 'AlleleParser::homopolymerRunRight' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:4111:32: performance:inconclusive: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace). [functionStatic]
freebayes-1.3.9/src/AlleleParser.h:296:22: note: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:4111:32: note: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:4163:20: performance:inconclusive: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
freebayes-1.3.9/src/AlleleParser.h:298:10: note: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:4163:20: note: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/AlleleParser.cpp:955:22: style:inconclusive: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:320:12: note: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:955:22: note: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:963:22: style:inconclusive: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:322:12: note: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:963:22: note: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:971:20: style:inconclusive: Technically the member function 'AlleleParser::isCpG' can be const. [functionConst]
freebayes-1.3.9/src/AlleleParser.h:329:10: note: Technically the member function 'AlleleParser::isCpG' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:971:20: note: Technically the member function 'AlleleParser::isCpG' can be const.
freebayes-1.3.9/src/AlleleParser.cpp:899:5: warning: Class 'AlleleParser' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
freebayes-1.3.9/src/AlleleParser.cpp:899:5: warning: Class 'AlleleParser' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
freebayes-1.3.9/src/NonCall.cpp:30:57: style:inconclusive: Function 'aggregatePerSample' argument 1 names different: declaration 'perSite' definition 'perSample'. [funcArgNamesDifferent]
freebayes-1.3.9/src/NonCall.h:45:51: note: Function 'aggregatePerSample' argument 1 names different: declaration 'perSite' definition 'perSample'.
freebayes-1.3.9/src/NonCall.cpp:30:57: note: Function 'aggregatePerSample' argument 1 names different: declaration 'perSite' definition 'perSample'.
freebayes-1.3.9/src/AlleleParser.cpp:2575:40: style: Condition 'currentPosition<allele->position' is always false [knownConditionTrueFalse]
freebayes-1.3.9/src/AlleleParser.cpp:2571:43: note: Assuming that condition 'allele->position<=currentPosition' is not redundant
freebayes-1.3.9/src/AlleleParser.cpp:2575:40: note: Condition 'currentPosition<allele->position' is always false
freebayes-1.3.9/src/AlleleParser.cpp:4048:41: style: Condition 'extend_left>0' is always true [knownConditionTrueFalse]
freebayes-1.3.9/src/AlleleParser.cpp:4040:41: note: Assuming that condition 'allele.position<=currentPosition' is not redundant
freebayes-1.3.9/src/AlleleParser.cpp:4045:64: note: Assignment 'extend_left=allele.position-currentPosition', assigned value is greater than 0
freebayes-1.3.9/src/AlleleParser.cpp:4048:41: note: Condition 'extend_left>0' is always true
freebayes-1.3.9/src/Parameters.cpp:7:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Parameters.cpp:29:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Parameters.cpp:502:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/AlleleParser.cpp:1977:14: style: The scope of the variable 'currentAlignment_end_position' can be reduced. [variableScope]
freebayes-1.3.9/src/AlleleParser.cpp:3177:14: style: The scope of the variable 'dividedIndel' can be reduced. [variableScope]
freebayes-1.3.9/src/AlleleParser.cpp:3582:21: style: The scope of the variable 'aptr' can be reduced. [variableScope]
freebayes-1.3.9/src/AlleleParser.cpp:639:74: style:inconclusive: Function 'loadNextPositionWithAlignmentOrInputVariant' argument 1 names different: declaration 'currentAlignment' definition 'alignment'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:208:64: note: Function 'loadNextPositionWithAlignmentOrInputVariant' argument 1 names different: declaration 'currentAlignment' definition 'alignment'.
freebayes-1.3.9/src/AlleleParser.cpp:639:74: note: Function 'loadNextPositionWithAlignmentOrInputVariant' argument 1 names different: declaration 'currentAlignment' definition 'alignment'.
freebayes-1.3.9/src/AlleleParser.cpp:967:47: style:inconclusive: Function 'referenceSubstr' argument 1 names different: declaration 'position' definition 'pos'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:239:37: note: Function 'referenceSubstr' argument 1 names different: declaration 'position' definition 'pos'.
freebayes-1.3.9/src/AlleleParser.cpp:967:47: note: Function 'referenceSubstr' argument 1 names different: declaration 'position' definition 'pos'.
freebayes-1.3.9/src/AlleleParser.cpp:967:65: style:inconclusive: Function 'referenceSubstr' argument 2 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:239:60: note: Function 'referenceSubstr' argument 2 names different: declaration 'length' definition 'len'.
freebayes-1.3.9/src/AlleleParser.cpp:967:65: note: Function 'referenceSubstr' argument 2 names different: declaration 'length' definition 'len'.
freebayes-1.3.9/src/AlleleParser.cpp:1001:44: style:inconclusive: Function 'addAllele' argument 1 names different: declaration 'allele' definition 'newAllele'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:75:27: note: Function 'addAllele' argument 1 names different: declaration 'allele' definition 'newAllele'.
freebayes-1.3.9/src/AlleleParser.cpp:1001:44: note: Function 'addAllele' argument 1 names different: declaration 'allele' definition 'newAllele'.
freebayes-1.3.9/src/AlleleParser.cpp:1175:42: style:inconclusive: Function 'makeAllele' argument 4 names different: declaration 'endpos' definition 'alignment_end_pos'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:182:32: note: Function 'makeAllele' argument 4 names different: declaration 'endpos' definition 'alignment_end_pos'.
freebayes-1.3.9/src/AlleleParser.cpp:1175:42: note: Function 'makeAllele' argument 4 names different: declaration 'endpos' definition 'alignment_end_pos'.
freebayes-1.3.9/src/AlleleParser.cpp:3041:44: style:inconclusive: Function 'fitHaplotype' argument 1 names different: declaration 'pos' definition 'haplotypeStart'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:77:27: note: Function 'fitHaplotype' argument 1 names different: declaration 'pos' definition 'haplotypeStart'.
freebayes-1.3.9/src/AlleleParser.cpp:3041:44: note: Function 'fitHaplotype' argument 1 names different: declaration 'pos' definition 'haplotypeStart'.
freebayes-1.3.9/src/AlleleParser.cpp:3217:14: style:inconclusive: Function 'buildHaplotypeAlleles' argument 2 names different: declaration 'allelesBySample' definition 'samples'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:281:41: note: Function 'buildHaplotypeAlleles' argument 2 names different: declaration 'allelesBySample' definition 'samples'.
freebayes-1.3.9/src/AlleleParser.cpp:3217:14: note: Function 'buildHaplotypeAlleles' argument 2 names different: declaration 'allelesBySample' definition 'samples'.
freebayes-1.3.9/src/AlleleParser.cpp:3668:44: style:inconclusive: Function 'getNextAlleles' argument 1 names different: declaration 'allelesBySample' definition 'samples'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:276:34: note: Function 'getNextAlleles' argument 1 names different: declaration 'allelesBySample' definition 'samples'.
freebayes-1.3.9/src/AlleleParser.cpp:3668:44: note: Function 'getNextAlleles' argument 1 names different: declaration 'allelesBySample' definition 'samples'.
freebayes-1.3.9/src/AlleleParser.cpp:3686:40: style:inconclusive: Function 'getAlleles' argument 1 names different: declaration 'allelesBySample' definition 'samples'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:287:30: note: Function 'getAlleles' argument 1 names different: declaration 'allelesBySample' definition 'samples'.
freebayes-1.3.9/src/AlleleParser.cpp:3686:40: note: Function 'getAlleles' argument 1 names different: declaration 'allelesBySample' definition 'samples'.
freebayes-1.3.9/src/AlleleParser.cpp:3688:36: style:inconclusive: Function 'getAlleles' argument 5 names different: declaration 'ignoreProcessedAlleles' definition 'ignoreProcessedFlag'. [funcArgNamesDifferent]
freebayes-1.3.9/src/AlleleParser.h:291:26: note: Function 'getAlleles' argument 5 names different: declaration 'ignoreProcessedAlleles' definition 'ignoreProcessedFlag'.
freebayes-1.3.9/src/AlleleParser.cpp:3688:36: note: Function 'getAlleles' argument 5 names different: declaration 'ignoreProcessedAlleles' definition 'ignoreProcessedFlag'.
freebayes-1.3.9/src/AlleleParser.cpp:1681:14: style: Local variable 'cigar' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/AlleleParser.cpp:1415:11: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:1681:14: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:1755:24: style: Local variable 'qualstr' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/AlleleParser.cpp:1733:20: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:1755:24: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:2154:75: style: Local variable 'f' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2129:67: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:2154:75: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:2242:24: style: Local variable 'genotypeAlleles' shadows outer function [shadowFunction]
freebayes-1.3.9/src/AlleleParser.h:306:20: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:2242:24: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:2365:26: style: Local variable 'pos' shadows outer argument [shadowArgument]
freebayes-1.3.9/src/AlleleParser.cpp:2327:49: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:2365:26: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:2376:32: style: Local variable 'genotypeAlleles' shadows outer function [shadowFunction]
freebayes-1.3.9/src/AlleleParser.h:306:20: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:2376:32: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:2965:66: style: Local variable 'v' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2961:50: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:2965:66: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:3910:17: style: Local variable 'genotypeAllele' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Allele.h:384:8: note: Shadowed declaration
freebayes-1.3.9/src/AlleleParser.cpp:3910:17: note: Shadow variable
freebayes-1.3.9/src/AlleleParser.cpp:3370:39: style: Argument 'std::max((long)0,(*h)->position-currentPosition)' to function string is always 0. It does not matter what value '(*h)->position' has. [knownArgument]
freebayes-1.3.9/src/AlleleParser.cpp:3367:36: note: Assuming that condition '(*h)->position==currentPosition' is not redundant
freebayes-1.3.9/src/AlleleParser.cpp:3370:39: note: Argument 'std::max((long)0,(*h)->position-currentPosition)' to function string is always 0. It does not matter what value '(*h)->position' has.
freebayes-1.3.9/src/AlleleParser.cpp:3370:66: style: Argument '(*h)->position-currentPosition' to function max is always 0. It does not matter what value '(*h)->position' has. [knownArgument]
freebayes-1.3.9/src/AlleleParser.cpp:3367:36: note: Assuming that condition '(*h)->position==currentPosition' is not redundant
freebayes-1.3.9/src/AlleleParser.cpp:3370:66: note: Argument '(*h)->position-currentPosition' to function max is always 0. It does not matter what value '(*h)->position' has.
freebayes-1.3.9/src/AlleleParser.cpp:1001:44: performance: Function parameter 'newAllele' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/AlleleParser.cpp:4083:45: performance: Function parameter 'altbase' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/AlleleParser.cpp:4097:46: performance: Function parameter 'altbase' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/AlleleParser.cpp:245:25: style: Variable 'sample' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:246:25: style: Variable 'population' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:525:17: style: Variable 'tech' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:674:50: style: Parameter 'seqname' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/AlleleParser.cpp:777:20: style: Variable 'bd' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:971:34: style: Parameter 'altbase' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/AlleleParser.cpp:1150:70: style: Parameter 'ref' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/AlleleParser.cpp:1150:83: style: Parameter 'alt' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/AlleleParser.cpp:1158:39: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:1252:27: style: Variable 'matchedRepeatCounts' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:1871:17: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:2195:37: style: Variable 'inChrom' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3018:17: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3226:17: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3288:25: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3498:31: style: Variable 'supported' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3542:41: style: Variable 'rq' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3608:37: style: Variable 'rq' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3859:26: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3874:21: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3879:21: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3920:34: style: Variable 'obs' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3923:29: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:3980:21: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/AlleleParser.cpp:2967:61: error: Iterator 'v' used after element has been erased. [eraseDereference]
freebayes-1.3.9/src/AlleleParser.cpp:2965:9: note: Iterator 'v' used after element has been erased.
freebayes-1.3.9/src/AlleleParser.cpp:2967:61: note: Iterator 'v' used after element has been erased.
freebayes-1.3.9/src/AlleleParser.cpp:169:14: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
freebayes-1.3.9/src/AlleleParser.cpp:305:14: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
freebayes-1.3.9/src/AlleleParser.cpp:376:31: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/AlleleParser.cpp:379:38: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/AlleleParser.cpp:1161:53: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/AlleleParser.cpp:3117:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/AlleleParser.cpp:1101:22: style: Unused variable: r [unusedVariable]
freebayes-1.3.9/src/AlleleParser.cpp:1560:28: style: Variable 'inMismatch' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2230:22: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2232:43: style: Variable 'includePreviousBaseForIndels' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2230:18: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2232:14: style: Variable 'includePreviousBaseForIndels' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2251:28: style: Unused variable: alleles [unusedVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2365:30: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2367:51: style: Variable 'includePreviousBaseForIndels' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2365:26: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2367:22: style: Variable 'includePreviousBaseForIndels' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2383:36: style: Unused variable: alleles [unusedVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2549:27: style: Variable 'requiredFlank' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:2549:13: style: Variable 'requiredFlank' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:3177:27: style: Variable 'dividedIndel' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:3188:34: style: Variable 'dividedIndel' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:3046:21: style: Unused variable: newAllelesPtr [unusedVariable]
freebayes-1.3.9/src/AlleleParser.cpp:3611:21: style: Unused variable: aptr [unusedVariable]
freebayes-1.3.9/src/AlleleParser.cpp:3631:21: style: Unused variable: partialObs [unusedVariable]
freebayes-1.3.9/src/AlleleParser.cpp:3869:28: style: Variable 'passesFilters' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/AlleleParser.cpp:3869:14: style: Variable 'passesFilters' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/Sample.cpp:349:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/ResultData.cpp:447:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/ResultData.cpp:660:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Sample.cpp:31:13: style:inconclusive: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const. [functionConst]
freebayes-1.3.9/src/Sample.h:71:9: note: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const.
freebayes-1.3.9/src/Sample.cpp:31:13: note: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const.
freebayes-1.3.9/src/Sample.cpp:376:18: style: The scope of the variable 'same' can be reduced. [variableScope]
freebayes-1.3.9/src/Sample.cpp:412:17: style: The scope of the variable 'sample' can be reduced. [variableScope]
freebayes-1.3.9/src/Sample.cpp:287:47: style:inconclusive: Function 'sufficientAlternateObservations' argument 1 names different: declaration 'observations' definition 'samples'. [funcArgNamesDifferent]
freebayes-1.3.9/src/Sample.h:132:47: note: Function 'sufficientAlternateObservations' argument 1 names different: declaration 'observations' definition 'samples'.
freebayes-1.3.9/src/Sample.cpp:287:47: note: Function 'sufficientAlternateObservations' argument 1 names different: declaration 'observations' definition 'samples'.
freebayes-1.3.9/src/Sample.cpp:198:34: style: Local variable 'g' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/Sample.cpp:192:27: note: Shadowed declaration
freebayes-1.3.9/src/Sample.cpp:198:34: note: Shadow variable
freebayes-1.3.9/src/Sample.cpp:202:37: style: Local variable 'alleles' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/Sample.cpp:194:26: note: Shadowed declaration
freebayes-1.3.9/src/Sample.cpp:202:37: note: Shadow variable
freebayes-1.3.9/src/Sample.cpp:214:32: performance: Function parameter 'refbase' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Sample.cpp:214:48: performance: Function parameter 'altbase' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Sample.cpp:244:30: performance: Function parameter 'base' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Sample.cpp:6:38: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:14:53: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:18:48: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:39:26: style: Variable 'supportingObs' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Sample.cpp:60:29: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:68:26: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Sample.cpp:76:39: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:84:26: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Sample.cpp:94:39: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:98:54: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:102:49: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:144:30: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:156:40: style: Parameter 'allele' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Sample.cpp:222:26: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Sample.cpp:248:26: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Sample.cpp:264:26: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Sample.cpp:302:30: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/Sample.cpp:41:32: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Sample.cpp:70:18: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Sample.cpp:86:18: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Sample.cpp:179:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Sample.cpp:251:19: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Sample.cpp:376:23: style: Variable 'same' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/Sample.cpp:400:22: style: Variable 'same' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/SegfaultHandler.cpp:15:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Parameters.cpp:388:13: warning: Member variable 'Parameters::allSites' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/Parameters.cpp:388:13: warning: Member variable 'Parameters::includeMonoB' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/Parameters.cpp:388:13: warning: Member variable 'Parameters::TR' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/Parameters.cpp:388:13: warning: Member variable 'Parameters::I' is not initialized in the constructor. [uninitMemberVar]
freebayes-1.3.9/src/Parameters.cpp:6:18: performance:inconclusive: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
freebayes-1.3.9/src/Parameters.h:136:10: note: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/Parameters.cpp:6:18: note: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace).
freebayes-1.3.9/src/Parameters.cpp:1121:9: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
freebayes-1.3.9/src/Parameters.cpp:498:9: style: The scope of the variable 'c' can be reduced. [variableScope]
freebayes-1.3.9/src/bamleftalign.cpp:27:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/bamleftalign.cpp:60:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/bamleftalign.cpp:42:9: style: The scope of the variable 'c' can be reduced. [variableScope]
freebayes-1.3.9/src/bamleftalign.cpp:48:10: style: The scope of the variable 'isuncompressed' can be reduced. [variableScope]
freebayes-1.3.9/src/bamleftalign.cpp:58:30: style: Variable 'long_options' can be declared as const array [constVariable]
freebayes-1.3.9/src/freebayes.cpp:105:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/freebayes.cpp:418:14: style: The scope of the variable 'bestOverallComboIsHet' can be reduced. [variableScope]
freebayes-1.3.9/src/freebayes.cpp:88:9: style: Local variable 'allowedAlleleTypes' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Allele.h:338:5: note: Shadowed declaration
freebayes-1.3.9/src/freebayes.cpp:88:9: note: Shadow variable
freebayes-1.3.9/src/freebayes.cpp:181:40: style: Local variable 'genotypesToErase' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/freebayes.cpp:178:36: note: Shadowed declaration
freebayes-1.3.9/src/freebayes.cpp:181:40: note: Shadow variable
freebayes-1.3.9/src/freebayes.cpp:555:35: style: Local variable 'allSampleDataLikelihoods' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/freebayes.cpp:422:47: note: Shadowed declaration
freebayes-1.3.9/src/freebayes.cpp:555:35: note: Shadow variable
freebayes-1.3.9/src/freebayes.cpp:612:28: style: Local variable 'alleles' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/freebayes.cpp:64:19: note: Shadowed declaration
freebayes-1.3.9/src/freebayes.cpp:612:28: note: Shadow variable
freebayes-1.3.9/src/freebayes.cpp:338:35: style: Variable 'genotypes' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/freebayes.cpp:587:25: style: Variable 'alt' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/freebayes.cpp:621:40: style: Variable 'sampleDataLikelihoods' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/freebayes.cpp:388:37: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/freebayes.cpp:626:67: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/freebayes.cpp:418:36: style: Variable 'bestOverallComboIsHet' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/freebayes.cpp:544:39: style: Variable 'bestOverallComboIsHet' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/freebayes.cpp:64:19: style: Unused variable: alleles [unusedVariable]
freebayes-1.3.9/src/freebayes.cpp:178:36: style: Unused variable: genotypesToErase [unusedVariable]
freebayes-1.3.9/src/freebayes.cpp:347:16: style: Variable 'estimatedMaxAlleleFrequency' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/freebayes.cpp:348:16: style: Variable 'estimatedMaxAlleleCount' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/freebayes.cpp:363:13: style: Variable 'inputLikelihoodCount' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/freebayes.cpp:422:47: style: Unused variable: allSampleDataLikelihoods [unusedVariable]
freebayes-1.3.9/src/ResultData.cpp:99:22: style: The scope of the variable 'refObsBySequencingTechnology' can be reduced. [variableScope]
freebayes-1.3.9/src/ResultData.cpp:15:21: style:inconclusive: Function 'vcf' argument 6 names different: declaration 'altAlleles' definition 'altAllelesIncludingNulls'. [funcArgNamesDifferent]
freebayes-1.3.9/src/ResultData.h:51:25: note: Function 'vcf' argument 6 names different: declaration 'altAlleles' definition 'altAllelesIncludingNulls'.
freebayes-1.3.9/src/ResultData.cpp:15:21: note: Function 'vcf' argument 6 names different: declaration 'altAlleles' definition 'altAllelesIncludingNulls'.
freebayes-1.3.9/src/ResultData.cpp:23:34: style:inconclusive: Function 'vcf' argument 14 names different: declaration 'partialSupport' definition 'partialObservationSupport'. [funcArgNamesDifferent]
freebayes-1.3.9/src/ResultData.h:59:38: note: Function 'vcf' argument 14 names different: declaration 'partialSupport' definition 'partialObservationSupport'.
freebayes-1.3.9/src/ResultData.cpp:23:34: note: Function 'vcf' argument 14 names different: declaration 'partialSupport' definition 'partialObservationSupport'.
freebayes-1.3.9/src/ResultData.cpp:642:15: style:inconclusive: Function 'gvcf' argument 2 names different: declaration 'noncalls' definition 'nonCalls'. [funcArgNamesDifferent]
freebayes-1.3.9/src/ResultData.h:66:19: note: Function 'gvcf' argument 2 names different: declaration 'noncalls' definition 'nonCalls'.
freebayes-1.3.9/src/ResultData.cpp:642:15: note: Function 'gvcf' argument 2 names different: declaration 'noncalls' definition 'nonCalls'.
freebayes-1.3.9/src/ResultData.cpp:259:49: style: Local variable 'f' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/ResultData.cpp:101:45: note: Shadowed declaration
freebayes-1.3.9/src/ResultData.cpp:259:49: note: Shadow variable
freebayes-1.3.9/src/ResultData.cpp:261:30: style: Local variable 'alternateAlleles' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Genotype.h:440:28: note: Shadowed declaration
freebayes-1.3.9/src/ResultData.cpp:261:30: note: Shadow variable
freebayes-1.3.9/src/ResultData.cpp:712:13: style: Local variable 'minDepth' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/ResultData.cpp:687:9: note: Shadowed declaration
freebayes-1.3.9/src/ResultData.cpp:712:13: note: Shadow variable
freebayes-1.3.9/src/ResultData.cpp:103:26: style: Variable 'referenceAlleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/ResultData.cpp:106:21: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/ResultData.cpp:261:30: style: Variable 'alternateAlleles' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/ResultData.cpp:265:25: style: Variable 'allele' can be declared as reference to const [constVariableReference]
freebayes-1.3.9/src/ResultData.cpp:447:27: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
freebayes-1.3.9/src/ResultData.cpp:427:33: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/ResultData.cpp:432:29: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/ResultData.cpp:476:29: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/ResultData.cpp:297:41: style: Variable 'altReadMismatchRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:298:36: style: Variable 'altReadSNPRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:299:38: style: Variable 'altReadIndelRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:404:32: style: Variable 'genotype' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:467:35: style: Variable 'genotypePtr' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:97:17: style: Variable 'refReadSoftClipSum' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:137:17: style: Variable 'refReadMismatchRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:138:17: style: Variable 'refReadSNPRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:139:17: style: Variable 'refReadIndelRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:162:16: style: Variable 'alternateQualitySum' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:163:16: style: Variable 'partialObservationCount' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:164:16: style: Unused variable: partialObservationQualitySum [unusedVariable]
freebayes-1.3.9/src/ResultData.cpp:297:21: style: Variable 'altReadMismatchRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:298:21: style: Variable 'altReadSNPRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:299:21: style: Variable 'altReadIndelRate' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:404:23: style: Variable 'genotype' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/ResultData.cpp:467:23: style: Variable 'genotypePtr' is assigned a value that is never used. [unreadVariable]
freebayes-1.3.9/src/Utility.cpp:185:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Utility.cpp:353:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LDBL_MIN_EXP [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Utility.cpp:588:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Utility.cpp:700:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
freebayes-1.3.9/src/Utility.cpp:552:16: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
freebayes-1.3.9/src/Utility.cpp:411:20: warning: Invalid std::log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
freebayes-1.3.9/src/Utility.cpp:407:23: note: Assignment 'sum=0', assigned value is 0
freebayes-1.3.9/src/Utility.cpp:408:65: note: Assuming condition is false
freebayes-1.3.9/src/Utility.cpp:411:20: note: Invalid argument
freebayes-1.3.9/src/Utility.cpp:376:14: style: Local variable 'sum' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Sum.h:7:3: note: Shadowed declaration
freebayes-1.3.9/src/Utility.cpp:376:14: note: Shadow variable
freebayes-1.3.9/src/Utility.cpp:377:46: style: Local variable 'i' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/Utility.cpp:369:41: note: Shadowed declaration
freebayes-1.3.9/src/Utility.cpp:377:46: note: Shadow variable
freebayes-1.3.9/src/Utility.cpp:407:17: style: Local variable 'sum' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Sum.h:7:3: note: Shadowed declaration
freebayes-1.3.9/src/Utility.cpp:407:17: note: Shadow variable
freebayes-1.3.9/src/Utility.cpp:408:46: style: Local variable 'i' shadows outer variable [shadowVariable]
freebayes-1.3.9/src/Utility.cpp:389:41: note: Shadowed declaration
freebayes-1.3.9/src/Utility.cpp:408:46: note: Shadow variable
freebayes-1.3.9/src/Utility.cpp:688:17: style: Local variable 'sum' shadows outer function [shadowFunction]
freebayes-1.3.9/src/Sum.h:7:3: note: Shadowed declaration
freebayes-1.3.9/src/Utility.cpp:688:17: note: Shadow variable
freebayes-1.3.9/src/Utility.cpp:155:28: performance: Function parameter 'item' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Utility.cpp:155:49: performance: Function parameter 'items' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Utility.cpp:457:43: performance: Function parameter 'source' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Utility.cpp:457:69: performance: Function parameter 'target' should be passed by const reference. [passedByValue]
freebayes-1.3.9/src/Utility.cpp:164:22: style: Parameter 's' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Utility.cpp:444:27: style: Parameter 'ref' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Utility.cpp:444:40: style: Parameter 'alt' can be declared as reference to const [constParameterReference]
freebayes-1.3.9/src/Utility.cpp:265:17: style: Variable 'cofactors' can be declared as const array [constVariable]
freebayes-1.3.9/src/Utility.cpp:548:16: style: Variable 'timeinfo' can be declared as pointer to const [constVariablePointer]
freebayes-1.3.9/src/Utility.cpp:150:14: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Utility.cpp:157:25: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Utility.cpp:378:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Utility.cpp:409:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Utility.cpp:690:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Utility.cpp:100746:19: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Utility.cpp:100754:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
freebayes-1.3.9/src/Utility.cpp:36:5: style: double result is returned as long double value. If the return value is long double to avoid loss of information, then you have loss of information. [truncLongCastReturn]
freebayes-1.3.9/src/Utility.cpp:426:5: style: double result is returned as long double value. If the return value is long double to avoid loss of information, then you have loss of information. [truncLongCastReturn]
freebayes-1.3.9/src/Utility.cpp:382:17: style: Unused variable: result [unusedVariable]
diff:
2.17.0 freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:273:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable iterator [valueFlowBailoutIncompleteVar]
head freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:277:18: style: Condition 'i->pos2<inext->pos2' is always true [knownConditionTrueFalse]
     freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:276:13: note: Assuming that condition 'i->pos2>=inext->pos2' is not redundant
     freebayes-1.3.9/contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp:277:18: note: Condition 'i->pos2<inext->pos2' is always true
2.17.0 freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:132:67: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:37: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:132:67: note: Null pointer addition
head freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:132:67: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:37: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:118:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:132:67: note: Null pointer addition
2.17.0 freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:292:20: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:37: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:292:20: note: Null pointer addition
head freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:292:20: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:37: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:250:21: note: Assignment 'oldd=(uint8_t*)malloc(b->l_data)', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/BamRecord.cpp:292:20: note: Null pointer addition
2.17.0 freebayes-1.3.9/contrib/SeqLib/src/ssw.c:213:27: error:inconclusive: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:213:27: note: Null pointer addition
head freebayes-1.3.9/contrib/SeqLib/src/ssw.c:213:27: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:213:27: note: Null pointer addition
2.17.0 freebayes-1.3.9/contrib/SeqLib/src/ssw.c:229:24: error:inconclusive: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:229:24: note: Null pointer addition
head freebayes-1.3.9/contrib/SeqLib/src/ssw.c:229:24: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:160:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:229:24: note: Null pointer addition
2.17.0 freebayes-1.3.9/contrib/SeqLib/src/ssw.c:444:27: error:inconclusive: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:444:27: note: Null pointer addition
head freebayes-1.3.9/contrib/SeqLib/src/ssw.c:444:27: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:444:27: note: Null pointer addition
2.17.0 freebayes-1.3.9/contrib/SeqLib/src/ssw.c:456:24: error:inconclusive: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:456:24: note: Null pointer addition
head freebayes-1.3.9/contrib/SeqLib/src/ssw.c:456:24: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:34: note: Assuming allocation function fails
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:401:17: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
     freebayes-1.3.9/contrib/SeqLib/src/ssw.c:456:24: note: Null pointer addition
head freebayes-1.3.9/src/Allele.cpp:1007:16: style:inconclusive: Technically the member function 'Allele::read3p' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:271:12: note: Technically the member function 'Allele::read3p' can be const.
     freebayes-1.3.9/src/Allele.cpp:1007:16: note: Technically the member function 'Allele::read3p' can be const.
head freebayes-1.3.9/src/Allele.cpp:1021:16: style:inconclusive: Technically the member function 'Allele::read5pNonNull' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:272:12: note: Technically the member function 'Allele::read5pNonNull' can be const.
     freebayes-1.3.9/src/Allele.cpp:1021:16: note: Technically the member function 'Allele::read5pNonNull' can be const.
head freebayes-1.3.9/src/Allele.cpp:1036:16: style:inconclusive: Technically the member function 'Allele::read3pNonNull' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:273:12: note: Technically the member function 'Allele::read3pNonNull' can be const.
     freebayes-1.3.9/src/Allele.cpp:1036:16: note: Technically the member function 'Allele::read3pNonNull' can be const.
head freebayes-1.3.9/src/Allele.cpp:1051:13: style:inconclusive: Technically the member function 'Allele::read5pNonNullBases' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:276:9: note: Technically the member function 'Allele::read5pNonNullBases' can be const.
     freebayes-1.3.9/src/Allele.cpp:1051:13: note: Technically the member function 'Allele::read5pNonNullBases' can be const.
head freebayes-1.3.9/src/Allele.cpp:1067:13: style:inconclusive: Technically the member function 'Allele::read3pNonNullBases' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:278:9: note: Technically the member function 'Allele::read3pNonNullBases' can be const.
     freebayes-1.3.9/src/Allele.cpp:1067:13: note: Technically the member function 'Allele::read3pNonNullBases' can be const.
head freebayes-1.3.9/src/Allele.cpp:1433:13: style:inconclusive: Technically the member function 'Allele::referenceLengthFromCigar' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:267:9: note: Technically the member function 'Allele::referenceLengthFromCigar' can be const.
     freebayes-1.3.9/src/Allele.cpp:1433:13: note: Technically the member function 'Allele::referenceLengthFromCigar' can be const.
head freebayes-1.3.9/src/Allele.cpp:18:13: style:inconclusive: Technically the member function 'Allele::bpLeft' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:311:9: note: Technically the member function 'Allele::bpLeft' can be const.
     freebayes-1.3.9/src/Allele.cpp:18:13: note: Technically the member function 'Allele::bpLeft' can be const.
head freebayes-1.3.9/src/Allele.cpp:22:13: style:inconclusive: Technically the member function 'Allele::bpRight' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:312:9: note: Technically the member function 'Allele::bpRight' can be const.
     freebayes-1.3.9/src/Allele.cpp:22:13: note: Technically the member function 'Allele::bpRight' can be const.
head freebayes-1.3.9/src/Allele.cpp:462:14: style:inconclusive: Technically the member function 'Allele::equivalent' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:239:10: note: Technically the member function 'Allele::equivalent' can be const.
     freebayes-1.3.9/src/Allele.cpp:462:14: note: Technically the member function 'Allele::equivalent' can be const.
head freebayes-1.3.9/src/Allele.cpp:845:14: style:inconclusive: Technically the member function 'Allele::sameSample' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.h:257:10: note: Technically the member function 'Allele::sameSample' can be const.
     freebayes-1.3.9/src/Allele.cpp:845:14: note: Technically the member function 'Allele::sameSample' can be const.
head freebayes-1.3.9/src/Allele.cpp:916:14: style: Variable 'allowed' is assigned a value that is never used. [unreadVariable]
2.17.0 freebayes-1.3.9/src/Allele.h:239:10: style:inconclusive: Technically the member function 'Allele::equivalent' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:462:14: note: Technically the member function 'Allele::equivalent' can be const.
     freebayes-1.3.9/src/Allele.h:239:10: note: Technically the member function 'Allele::equivalent' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:257:10: style:inconclusive: Technically the member function 'Allele::sameSample' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:845:14: note: Technically the member function 'Allele::sameSample' can be const.
     freebayes-1.3.9/src/Allele.h:257:10: note: Technically the member function 'Allele::sameSample' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:267:9: style:inconclusive: Technically the member function 'Allele::referenceLengthFromCigar' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:1433:13: note: Technically the member function 'Allele::referenceLengthFromCigar' can be const.
     freebayes-1.3.9/src/Allele.h:267:9: note: Technically the member function 'Allele::referenceLengthFromCigar' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:271:12: style:inconclusive: Technically the member function 'Allele::read3p' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:1007:16: note: Technically the member function 'Allele::read3p' can be const.
     freebayes-1.3.9/src/Allele.h:271:12: note: Technically the member function 'Allele::read3p' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:272:12: style:inconclusive: Technically the member function 'Allele::read5pNonNull' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:1021:16: note: Technically the member function 'Allele::read5pNonNull' can be const.
     freebayes-1.3.9/src/Allele.h:272:12: note: Technically the member function 'Allele::read5pNonNull' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:273:12: style:inconclusive: Technically the member function 'Allele::read3pNonNull' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:1036:16: note: Technically the member function 'Allele::read3pNonNull' can be const.
     freebayes-1.3.9/src/Allele.h:273:12: note: Technically the member function 'Allele::read3pNonNull' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:276:9: style:inconclusive: Technically the member function 'Allele::read5pNonNullBases' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:1051:13: note: Technically the member function 'Allele::read5pNonNullBases' can be const.
     freebayes-1.3.9/src/Allele.h:276:9: note: Technically the member function 'Allele::read5pNonNullBases' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:278:9: style:inconclusive: Technically the member function 'Allele::read3pNonNullBases' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:1067:13: note: Technically the member function 'Allele::read3pNonNullBases' can be const.
     freebayes-1.3.9/src/Allele.h:278:9: note: Technically the member function 'Allele::read3pNonNullBases' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:311:9: style:inconclusive: Technically the member function 'Allele::bpLeft' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:18:13: note: Technically the member function 'Allele::bpLeft' can be const.
     freebayes-1.3.9/src/Allele.h:311:9: note: Technically the member function 'Allele::bpLeft' can be const.
2.17.0 freebayes-1.3.9/src/Allele.h:312:9: style:inconclusive: Technically the member function 'Allele::bpRight' can be const. [functionConst]
     freebayes-1.3.9/src/Allele.cpp:22:13: note: Technically the member function 'Allele::bpRight' can be const.
     freebayes-1.3.9/src/Allele.h:312:9: note: Technically the member function 'Allele::bpRight' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:2230:18: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/AlleleParser.cpp:2232:14: style: Variable 'includePreviousBaseForIndels' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/AlleleParser.cpp:2365:26: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/AlleleParser.cpp:2367:22: style: Variable 'includePreviousBaseForIndels' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/AlleleParser.cpp:2542:20: style:inconclusive: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:250:10: note: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:2542:20: note: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:2549:13: style: Variable 'requiredFlank' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/AlleleParser.cpp:2562:20: style:inconclusive: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:251:10: note: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:2562:20: note: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:2596:20: style:inconclusive: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:257:10: note: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:2596:20: note: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:2606:20: performance:inconclusive: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.h:254:10: note: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.cpp:2606:20: note: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace).
head freebayes-1.3.9/src/AlleleParser.cpp:2617:20: performance:inconclusive: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.h:255:10: note: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.cpp:2617:20: note: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace).
head freebayes-1.3.9/src/AlleleParser.cpp:3869:14: style: Variable 'passesFilters' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/AlleleParser.cpp:4083:19: style:inconclusive: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:294:9: note: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:4083:19: note: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:4097:19: style:inconclusive: Technically the member function 'AlleleParser::homopolymerRunRight' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:295:9: note: Technically the member function 'AlleleParser::homopolymerRunRight' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:4097:19: note: Technically the member function 'AlleleParser::homopolymerRunRight' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:4111:32: performance:inconclusive: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.h:296:22: note: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.cpp:4111:32: note: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace).
head freebayes-1.3.9/src/AlleleParser.cpp:4163:20: performance:inconclusive: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.h:298:10: note: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.cpp:4163:20: note: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace).
head freebayes-1.3.9/src/AlleleParser.cpp:942:19: style:inconclusive: Technically the member function 'AlleleParser::currentSequencePosition' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:273:9: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:942:19: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:947:19: style:inconclusive: Technically the member function 'AlleleParser::currentSequencePosition' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:274:9: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:947:19: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:955:22: style:inconclusive: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:320:12: note: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:955:22: note: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:963:22: style:inconclusive: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:322:12: note: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:963:22: note: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const.
head freebayes-1.3.9/src/AlleleParser.cpp:971:20: style:inconclusive: Technically the member function 'AlleleParser::isCpG' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.h:329:10: note: Technically the member function 'AlleleParser::isCpG' can be const.
     freebayes-1.3.9/src/AlleleParser.cpp:971:20: note: Technically the member function 'AlleleParser::isCpG' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:250:10: style:inconclusive: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:2542:20: note: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const.
     freebayes-1.3.9/src/AlleleParser.h:250:10: note: Technically the member function 'AlleleParser::removeAllelesWithoutReadSpan' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:251:10: style:inconclusive: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:2562:20: note: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const.
     freebayes-1.3.9/src/AlleleParser.h:251:10: note: Technically the member function 'AlleleParser::removeNonOverlappingAlleles' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:254:10: performance:inconclusive: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.cpp:2606:20: note: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.h:254:10: note: Technically the member function 'AlleleParser::removePreviousAlleles' can be static (but you may consider moving to unnamed namespace).
2.17.0 freebayes-1.3.9/src/AlleleParser.h:255:10: performance:inconclusive: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.cpp:2617:20: note: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.h:255:10: note: Technically the member function 'AlleleParser::removeCoverageSkippedAlleles' can be static (but you may consider moving to unnamed namespace).
2.17.0 freebayes-1.3.9/src/AlleleParser.h:257:10: style:inconclusive: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:2596:20: note: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const.
     freebayes-1.3.9/src/AlleleParser.h:257:10: note: Technically the member function 'AlleleParser::removeFilteredAlleles' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:273:9: style:inconclusive: Technically the member function 'AlleleParser::currentSequencePosition' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:942:19: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
     freebayes-1.3.9/src/AlleleParser.h:273:9: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:274:9: style:inconclusive: Technically the member function 'AlleleParser::currentSequencePosition' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:947:19: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
     freebayes-1.3.9/src/AlleleParser.h:274:9: note: Technically the member function 'AlleleParser::currentSequencePosition' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:294:9: style:inconclusive: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:4083:19: note: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const.
     freebayes-1.3.9/src/AlleleParser.h:294:9: note: Technically the member function 'AlleleParser::homopolymerRunLeft' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:295:9: style:inconclusive: Technically the member function 'AlleleParser::homopolymerRunRight' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:4097:19: note: Technically the member function 'AlleleParser::homopolymerRunRight' can be const.
     freebayes-1.3.9/src/AlleleParser.h:295:9: note: Technically the member function 'AlleleParser::homopolymerRunRight' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:296:22: performance:inconclusive: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.cpp:4111:32: note: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.h:296:22: note: Technically the member function 'AlleleParser::repeatCounts' can be static (but you may consider moving to unnamed namespace).
2.17.0 freebayes-1.3.9/src/AlleleParser.h:298:10: performance:inconclusive: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/AlleleParser.cpp:4163:20: note: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/AlleleParser.h:298:10: note: Technically the member function 'AlleleParser::isRepeatUnit' can be static (but you may consider moving to unnamed namespace).
2.17.0 freebayes-1.3.9/src/AlleleParser.h:320:12: style:inconclusive: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:955:22: note: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const.
     freebayes-1.3.9/src/AlleleParser.h:320:12: note: Technically the member function 'AlleleParser::currentReferenceBaseString' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:322:12: style:inconclusive: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:963:22: note: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const.
     freebayes-1.3.9/src/AlleleParser.h:322:12: note: Technically the member function 'AlleleParser::currentReferenceHaplotype' can be const.
2.17.0 freebayes-1.3.9/src/AlleleParser.h:329:10: style:inconclusive: Technically the member function 'AlleleParser::isCpG' can be const. [functionConst]
     freebayes-1.3.9/src/AlleleParser.cpp:971:20: note: Technically the member function 'AlleleParser::isCpG' can be const.
     freebayes-1.3.9/src/AlleleParser.h:329:10: note: Technically the member function 'AlleleParser::isCpG' can be const.
head freebayes-1.3.9/src/Bias.cpp:48:12: style:inconclusive: Technically the member function 'Bias::empty' can be const. [functionConst]
     freebayes-1.3.9/src/Bias.h:25:10: note: Technically the member function 'Bias::empty' can be const.
     freebayes-1.3.9/src/Bias.cpp:48:12: note: Technically the member function 'Bias::empty' can be const.
2.17.0 freebayes-1.3.9/src/Bias.h:25:10: style:inconclusive: Technically the member function 'Bias::empty' can be const. [functionConst]
     freebayes-1.3.9/src/Bias.cpp:48:12: note: Technically the member function 'Bias::empty' can be const.
     freebayes-1.3.9/src/Bias.h:25:10: note: Technically the member function 'Bias::empty' can be const.
head freebayes-1.3.9/src/DataLikelihood.cpp:19:9: style: Variable 'observationCount' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/DataLikelihood.cpp:23:12: style: Variable 'countIn' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/DataLikelihood.cpp:73:29: style: Variable 'probi' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/FBFasta.cpp:218:24: performance:inconclusive: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static. [functionStatic]
     freebayes-1.3.9/src/FBFasta.h:59:16: note: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static.
     freebayes-1.3.9/src/FBFasta.cpp:218:24: note: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static.
head freebayes-1.3.9/src/FBFasta.cpp:265:12: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/FBFasta.cpp:265:22: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:265:22: note: Null pointer dereference
head freebayes-1.3.9/src/FBFasta.cpp:266:5: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:266:5: note: Null pointer dereference
head freebayes-1.3.9/src/FBFasta.cpp:268:22: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:268:22: note: Null pointer addition
head freebayes-1.3.9/src/FBFasta.cpp:271:16: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:263:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:263:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:271:16: note: Null pointer dereference
head freebayes-1.3.9/src/FBFasta.cpp:283:28: style:inconclusive: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const. [functionConst]
     freebayes-1.3.9/src/FBFasta.h:78:16: note: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const.
     freebayes-1.3.9/src/FBFasta.cpp:283:28: note: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const.
head freebayes-1.3.9/src/FBFasta.cpp:308:12: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/FBFasta.cpp:308:22: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:308:22: note: Null pointer dereference
head freebayes-1.3.9/src/FBFasta.cpp:309:5: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:309:5: note: Null pointer dereference
head freebayes-1.3.9/src/FBFasta.cpp:311:22: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:311:22: note: Null pointer addition
head freebayes-1.3.9/src/FBFasta.cpp:314:16: warning: If memory allocation fails, then there is a possible null pointer dereference: seq [nullPointerOutOfMemory]
     freebayes-1.3.9/src/FBFasta.cpp:306:32: note: Assuming allocation function fails
     freebayes-1.3.9/src/FBFasta.cpp:306:17: note: Assignment 'seq=(char*)std::calloc(seqlen+1,sizeof(char))', assigned value is 0
     freebayes-1.3.9/src/FBFasta.cpp:314:16: note: Null pointer dereference
2.17.0 freebayes-1.3.9/src/FBFasta.h:59:16: performance:inconclusive: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static. [functionStatic]
     freebayes-1.3.9/src/FBFasta.cpp:218:24: note: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static.
     freebayes-1.3.9/src/FBFasta.h:59:16: note: Either there is a missing 'override', or the member function 'FB::FastaIndex::indexFileExtension' can be static.
2.17.0 freebayes-1.3.9/src/FBFasta.h:78:16: style:inconclusive: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const. [functionConst]
     freebayes-1.3.9/src/FBFasta.cpp:283:28: note: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const.
     freebayes-1.3.9/src/FBFasta.h:78:16: note: Technically the member function 'FB::FastaReference::sequenceNameStartingWith' can be const.
head freebayes-1.3.9/src/Genotype.cpp:693:21: style:inconclusive: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const. [functionConst]
     freebayes-1.3.9/src/Genotype.h:218:10: note: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const.
     freebayes-1.3.9/src/Genotype.cpp:693:21: note: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const.
2.17.0 freebayes-1.3.9/src/Genotype.h:218:10: style:inconclusive: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const. [functionConst]
     freebayes-1.3.9/src/Genotype.cpp:693:21: note: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const.
     freebayes-1.3.9/src/Genotype.h:218:10: note: Either there is a missing 'override', or the member function 'GenotypeCombo::isHomozygous' can be const.
head freebayes-1.3.9/src/Parameters.cpp:6:18: performance:inconclusive: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/Parameters.h:136:10: note: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/Parameters.cpp:6:18: note: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace).
2.17.0 freebayes-1.3.9/src/Parameters.h:136:10: performance:inconclusive: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     freebayes-1.3.9/src/Parameters.cpp:6:18: note: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace).
     freebayes-1.3.9/src/Parameters.h:136:10: note: Technically the member function 'Parameters::simpleUsage' can be static (but you may consider moving to unnamed namespace).
head freebayes-1.3.9/src/ResultData.cpp:297:21: style: Variable 'altReadMismatchRate' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/ResultData.cpp:298:21: style: Variable 'altReadSNPRate' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/ResultData.cpp:299:21: style: Variable 'altReadIndelRate' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/ResultData.cpp:404:23: style: Variable 'genotype' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/ResultData.cpp:467:23: style: Variable 'genotypePtr' is assigned a value that is never used. [unreadVariable]
head freebayes-1.3.9/src/Sample.cpp:31:13: style:inconclusive: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const. [functionConst]
     freebayes-1.3.9/src/Sample.h:71:9: note: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const.
     freebayes-1.3.9/src/Sample.cpp:31:13: note: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const.
2.17.0 freebayes-1.3.9/src/Sample.h:71:9: style:inconclusive: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const. [functionConst]
     freebayes-1.3.9/src/Sample.cpp:31:13: note: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const.
     freebayes-1.3.9/src/Sample.h:71:9: note: Either there is a missing 'override', or the member function 'Sample::partialObservationCount' can be const.


DONE