2025-05-09 12:44
ftp://ftp.de.debian.org/debian/pool/main/b/bowtie/bowtie_1.3.1.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 -j1
platform: Linux-6.8.0-59-generic-x86_64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 14.2.0-4ubuntu2~24.04) 14.2.0
cppcheck: head 2.17.0
head-info: d655a3a (2025-05-09 12:19:47 +0200)
count: 1711 1702
elapsed-time: 259.4 270.6
head-timing-info:

old-timing-info:

head results:
bowtie-1.3.1/assert_helpers.h:232:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/assert_helpers.h:250:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/alphabet.h:212:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/alphabet.h:213:16: warning: Either the condition '(c)<=4' is redundant or the array 'dnacomp[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie-1.3.1/alphabet.h:212:2: note: Assuming that condition '(c)<=4' is not redundant
bowtie-1.3.1/alphabet.h:213:16: note: Array index out of bounds
bowtie-1.3.1/assert_helpers.h:14:2: style: Class 'ReleaseAssertException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/bt2_locks.h:61:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bt2_locks.h:67:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/random_source.h:39:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:85:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:122:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1050:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1059:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1079:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1094:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1119:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1179:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1187:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1195:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1259:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1289:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1330:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1353:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1394:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1403:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1423:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1438:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1461:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1519:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1527:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1535:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1548:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1556:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1599:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1629:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1670:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1693:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1739:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1751:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1764:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1786:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1793:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1897:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1924:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1972:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2015:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2032:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2079:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2088:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2108:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2123:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2148:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2237:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2245:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2293:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2323:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2361:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2384:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2432:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2514:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2533:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2557:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2574:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2597:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2626:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2645:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2687:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2704:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2937:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:2945:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3136:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3175:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3192:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3215:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3233:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3259:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3268:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3282:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3292:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3304:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3315:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3327:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3349:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3410:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3430:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3439:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3448:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3457:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3481:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3542:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3562:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3571:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3580:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3589:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3613:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3854:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3891:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3943:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:3963:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:4168:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/tokenize.h:31:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_build_main.cpp:51:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:355:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:364:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:383:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:395:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:421:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:513:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:533:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:592:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:603:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:619:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:633:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:649:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:665:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:687:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:695:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:750:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:758:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:796:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:805:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:841:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:866:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:886:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:912:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:938:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:1001:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:4064:11: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie-1.3.1/ds.h:4086:13: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie-1.3.1/ds.h:4112:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie-1.3.1/ds.h:4113:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie-1.3.1/ds.h:4125:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie-1.3.1/ds.h:4126:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie-1.3.1/ds.h:4132:10: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie-1.3.1/random_source.h:20:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/random_source.h:20:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/random_source.h:22:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/random_source.h:24:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/random_source.h:24:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ds.h:1763:8: warning: Member variable 'ESet::cat_' is not assigned a value in 'ESet::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:2451:8: warning: Member variable 'EMap::cat_' is not assigned a value in 'EMap::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < uint8_t * , 128 >::cat_' is not assigned a value in 'EList < uint8_t * , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < string , 128 >::cat_' is not assigned a value in 'EList < string , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < std :: string , 128 >::cat_' is not assigned a value in 'EList < std :: string , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:4195:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4195:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4220:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4220:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4220:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4245:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4245:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4245:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ds.h:4245:43: performance: Variable 'd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/bt2_locks.h:59:7: performance:inconclusive: Technically the member function 'mcs_lock::spin_while_eq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/bt2_locks.h:65:7: performance:inconclusive: Technically the member function 'mcs_lock::spin_while_eq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:59:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
bowtie-1.3.1/ds.h:65:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
bowtie-1.3.1/ds.h:70:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
bowtie-1.3.1/ds.h:76:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
bowtie-1.3.1/ds.h:1202:29: performance:inconclusive: Technically the member function 'ELList::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:1542:34: performance:inconclusive: Technically the member function 'ELLList::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:2231:24: performance:inconclusive: Technically the member function 'ELSet::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:3126:7: performance:inconclusive: Technically the member function 'Pool::free' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint8_t * , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < uint8_t * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < string , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < string , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: string , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: string , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:116:3: warning: Class 'AutoArray' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/ds.h:116:3: warning: Class 'AutoArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/ds.h:3078:3: warning: Class 'Pool' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/ds.h:3078:3: warning: Class 'Pool' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/threading.h:84:2: style: Class 'ThreadSafe' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/random_source.h:22:2: style: Class 'RandomSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:114:2: style: Class 'AutoArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:1716:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:1733:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:2411:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:2426:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:3164:2: style: Class 'PList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:3771:2: style: Class 'RedBlack' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/bowtie_build_main.cpp:44:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
bowtie-1.3.1/bowtie_build_main.cpp:42:46: note: Assuming allocation function fails
bowtie-1.3.1/bowtie_build_main.cpp:42:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
bowtie-1.3.1/bowtie_build_main.cpp:44:5: note: Null pointer dereference
bowtie-1.3.1/ds.h:3371:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ds.h:4139:14: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/bowtie_build_main.cpp:42:27: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ds.h:603:3: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ds.h:3214:14: style: Local variable 'i' shadows outer argument [shadowArgument]
bowtie-1.3.1/ds.h:3210:10: note: Shadowed declaration
bowtie-1.3.1/ds.h:3214:14: note: Shadow variable
bowtie-1.3.1/ds.h:3695:34: style: Parameter 'ol' can be declared as pointer to const [constParameterPointer]
bowtie-1.3.1/sstring.h:2901:37: debug: Failed to instantiate template "SStringExpandable". The checking continues anyway. [templateInstantiation]
bowtie-1.3.1/blockwise_sa.h:434:8: debug: Failed to instantiate template "EList". The checking continues anyway. [templateInstantiation]
bowtie-1.3.1/bitpack.h:13:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitpack.h:19:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitpack.h:24:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitpack.h:30:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:28:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:66:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:113:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:133:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:172:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:211:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:229:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:425:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:435:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:450:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:466:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/util.h:38:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_signed [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/util.h:59:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:121:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:204:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:231:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:303:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:329:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:374:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:400:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:445:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:471:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1059:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1076:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1094:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1124:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1132:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1140:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1453:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1483:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1529:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1550:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2247:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2255:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2286:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2312:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2326:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2334:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2342:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2354:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2369:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2381:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2445:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2461:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2470:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2483:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2500:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2522:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2575:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2688:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2701:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2713:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2731:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2747:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2762:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2792:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2802:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2812:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2821:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2830:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2846:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2862:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2879:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3255:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3270:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3284:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3302:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3318:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3341:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3350:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3361:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3370:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3381:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3403:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3412:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3427:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3444:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3465:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/binary_sa_search.h:38:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:110:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:200:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:221:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:324:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:338:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:356:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:475:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:541:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:552:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:581:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:612:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:628:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:637:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:652:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:678:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:704:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:728:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:757:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/filebuf.h:772:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/qual.h:30:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/qual.h:91:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/qual.h:148:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/edit.h:42:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.h:39:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.h:61:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.h:220:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.h:248:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.h:364:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stratum [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.h:402:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable h [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/read.h:211:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/read.h:223:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/read.h:232:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/read.h:244:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/read.h:323:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alignment [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:115:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:135:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:143:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:160:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:224:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:331:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:351:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:428:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:511:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:578:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:613:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:727:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:788:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.h:896:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sequence_io.h:26:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sequence_io.h:65:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sequence_io.h:162:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:21:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:33:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:93:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:111:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:135:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:154:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:244:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:283:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:302:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:338:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:400:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:481:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:516:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:650:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:675:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:706:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:770:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:802:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:892:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:1041:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/multikey_qsort.h:1138:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/timer.h:121:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/timer.h:145:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:70:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:111:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:154:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:281:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:409:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:472:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:496:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:508:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:645:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:807:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/word_io.h:28:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/word_io.h:48:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/word_io.h:54:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/word_io.h:92:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/zbox.h:23:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:478:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:742:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:804:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:86:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:184:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable batchId [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:237:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:303:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:518:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable batchId [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:636:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:732:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:768:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:797:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable patId [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:830:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:1106:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable oms [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:1270:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_read.h:66:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_read.h:149:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:65:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:389:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:431:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:496:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:655:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:663:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:669:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:675:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/reference.h:681:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:95:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:242:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:258:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:337:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:440:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:501:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:587:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:642:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:828:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:899:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:992:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1026:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1048:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1074:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1165:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1252:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1313:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1447:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1481:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner_metrics.h:123:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner_metrics.h:203:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:21:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:71:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:93:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:207:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:241:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:254:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:295:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_util.h:317:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range.h:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/log.h:13:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/log.h:18:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:36:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:65:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:79:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:87:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:118:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:148:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:35:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:78:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:95:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:108:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:230:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:334:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:494:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:551:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:628:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:658:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:785:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:861:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:915:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:962:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:977:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1041:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1132:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1242:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1265:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1329:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1339:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1363:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1396:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1427:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1441:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1477:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1900:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1950:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1963:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1974:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:118:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:149:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:171:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:238:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:322:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:378:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1128:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1173:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1186:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1206:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1298:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1330:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1352:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1375:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1395:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1439:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1460:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1528:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1574:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1679:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1826:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable curEbwt_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1849:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1884:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:1923:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2068:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2407:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2454:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2512:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2534:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2707:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2724:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2823:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2964:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2985:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable foundRange [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search_backtrack.h:3012:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1541:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1563:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1591:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:1636:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2035:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2083:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2137:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2185:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2246:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2309:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2346:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2392:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2430:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2466:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2503:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2539:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2581:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2651:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/row_chaser.h:70:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/row_chaser.h:109:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/row_chaser.h:134:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/row_chaser.h:155:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2710:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2770:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2813:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:2849:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3457:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3547:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3558:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3634:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3683:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3760:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3800:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3839:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt.h:3994:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:54:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:91:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:116:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:147:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:202:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:255:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:343:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:378:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:413:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:479:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2055:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable foundRange [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2077:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2099:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable foundRange [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2145:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable minCost [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2159:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable minCost [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2289:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2314:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable foundRange [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2402:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:2430:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1751:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1778:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable done [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_source.h:1648:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:199:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:243:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:327:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:336:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:367:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pool.h:374:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:252:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:283:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:383:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:449:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:547:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:763:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:836:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:941:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:93:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:543:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:604:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:668:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:707:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:830:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:1006:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:1017:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:1036:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/diff_sample.h:1079:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2973:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2986:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2998:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3035:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3050:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3064:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3093:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3102:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3113:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3122:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3133:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3152:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3158:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3173:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:3190:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1717:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1733:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1759:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1774:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1790:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1802:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1810:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1818:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1918:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1956:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:1973:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2040:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:2056:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:628:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:644:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:655:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:663:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:671:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:679:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:789:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:803:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:844:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:317:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:327:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bitset.h:343:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:687:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:758:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:857:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable list_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ds.h:879:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur_ [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/blockwise_sa.h:524:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_inspect.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie-1.3.1/ebwt_search_backtrack.h:2997:11: warning: Assert statement calls a function which may have desired side effects: 'range'. [assertWithSideEffect]
bowtie-1.3.1/ebwt.h:3532:9: warning: Assert statement calls a function which may have desired side effects: 'ferror'. [assertWithSideEffect]
bowtie-1.3.1/range_source.h:1826:11: warning: Assert statement calls a function which may have desired side effects: 'range'. [assertWithSideEffect]
bowtie-1.3.1/range_source.h:1649:11: warning: Assert statement calls a function which may have desired side effects: 'range'. [assertWithSideEffect]
bowtie-1.3.1/multikey_qsort.h:1071:16: warning: Either the condition '(c)<=4' is redundant or the array 'bkts[4]' is accessed at index 4, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie-1.3.1/multikey_qsort.h:1067:4: note: Assuming that condition '(c)<=4' is not redundant
bowtie-1.3.1/multikey_qsort.h:1071:16: note: Array index out of bounds
bowtie-1.3.1/multikey_qsort.h:1071:26: warning: Either the condition '(c)<=4' is redundant or the array 'cnts[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie-1.3.1/multikey_qsort.h:1067:4: note: Assuming that condition '(c)<=4' is not redundant
bowtie-1.3.1/multikey_qsort.h:1071:26: note: Array index out of bounds
bowtie-1.3.1/aligner_metrics.h:205:6: warning: Either the condition 'c<5' is redundant or the array 'cs[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie-1.3.1/aligner_metrics.h:203:4: note: Assuming that condition 'c<5' is not redundant
bowtie-1.3.1/aligner_metrics.h:205:6: note: Array index out of bounds
bowtie-1.3.1/aligner_metrics.h:205:6: warning: Either the condition '(c)>=0' is redundant or the array 'cs[5]' is accessed at index -1, which is out of bounds. [negativeIndex]
bowtie-1.3.1/aligner_metrics.h:204:4: note: Assuming that condition '(c)>=0' is not redundant
bowtie-1.3.1/aligner_metrics.h:205:6: note: Negative array index
bowtie-1.3.1/ebwt_search_backtrack.h:2208:16: warning: Either the condition 'cc<4' is redundant or the array 'rs->tops[4]' is accessed at index 4, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie-1.3.1/ebwt_search_backtrack.h:2207:8: note: Assuming that condition 'cc<4' is not redundant
bowtie-1.3.1/ebwt_search_backtrack.h:2208:16: note: Array index out of bounds
bowtie-1.3.1/ebwt_search_backtrack.h:2209:16: warning: Either the condition 'cc<4' is redundant or the array 'rs->bots[4]' is accessed at index 4, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie-1.3.1/ebwt_search_backtrack.h:2207:8: note: Assuming that condition 'cc<4' is not redundant
bowtie-1.3.1/ebwt_search_backtrack.h:2209:16: note: Array index out of bounds
bowtie-1.3.1/timer.h:137:12: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
bowtie-1.3.1/filebuf.h:392:18: warning: Either the condition 'c==-1' is redundant or isspace() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
bowtie-1.3.1/filebuf.h:394:21: note: Assuming that condition 'c==-1' is not redundant
bowtie-1.3.1/filebuf.h:392:18: note: Invalid argument
bowtie-1.3.1/filebuf.h:431:18: warning: Either the condition 'c==-1' is redundant or isspace() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
bowtie-1.3.1/filebuf.h:433:21: note: Assuming that condition 'c==-1' is not redundant
bowtie-1.3.1/filebuf.h:431:18: note: Invalid argument
bowtie-1.3.1/ref_read.h:195:3: warning: Either the condition '-1!=(lastc)' is redundant or std::toupper() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
bowtie-1.3.1/ref_read.h:154:2: note: Assuming that condition '-1!=(lastc)' is not redundant
bowtie-1.3.1/ref_read.h:165:4: note: c is assigned 'lastc' here.
bowtie-1.3.1/ref_read.h:195:3: note: Invalid argument
bowtie-1.3.1/ds.h:534:3: error: Using 'memset' on struct that contains a 'std::pair'. [memsetClass]
bowtie-1.3.1/ds.h:541:3: error: Using 'memset' on struct that contains a 'std::pair'. [memsetClass]
bowtie-1.3.1/ds.h:534:3: error: Using 'memset' on class that contains a virtual function. [memsetClass]
bowtie-1.3.1/ds.h:541:3: error: Using 'memset' on class that contains a virtual function. [memsetClass]
bowtie-1.3.1/ds.h:534:3: error: Using 'memset' on class that contains a 'std::pair'. [memsetClass]
bowtie-1.3.1/ds.h:541:3: error: Using 'memset' on class that contains a 'std::pair'. [memsetClass]
bowtie-1.3.1/sstring.h:2197:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:2209:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:2216:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:2223:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:2295:21: warning: Member variable 'SStringFixed::printcs_' is not assigned a value in 'SStringFixed::operator='. [operatorEqVarError]
bowtie-1.3.1/filebuf.h:66:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:66:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:70:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:70:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:76:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:76:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:82:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:82:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:88:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:88:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:607:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:622:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/filebuf.h:636:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/edit.h:33:2: warning: Member variable 'Edit::chr' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/edit.h:33:2: warning: Member variable 'Edit::qchr' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/edit.h:33:2: warning: Member variable 'Edit::type' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/edit.h:33:2: warning: Member variable 'Edit::reserved' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/edit.h:35:2: warning: Member variable 'Edit::reserved' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit_set.h:29:2: warning: Member variable 'HitSetEnt::fw' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit_set.h:29:2: warning: Member variable 'HitSetEnt::stratum' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit_set.h:29:2: warning: Member variable 'HitSetEnt::cost' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit_set.h:29:2: warning: Member variable 'HitSetEnt::oms' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:46:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:46:2: warning: Member variable 'Read::primer' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:46:2: warning: Member variable 'Read::trimc' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:48:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:48:2: warning: Member variable 'Read::primer' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:48:2: warning: Member variable 'Read::trimc' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:347:2: warning: Member variable 'PerReadMetrics::tz_beg' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:347:2: warning: Member variable 'PerReadMetrics::seedPctUniqueMS' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:347:2: warning: Member variable 'PerReadMetrics::seedPctRepMS' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:347:2: warning: Member variable 'PerReadMetrics::seedHitAvgMS' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/read.h:347:2: warning: Member variable 'PerReadMetrics::seedsPerNucMS' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::format' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::fileParallel' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::seed' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::max_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::solexa64' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::phred64' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::intQuals' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::sampleLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::sampleFreq' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::skip' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::nthreads' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:47:2: warning:inconclusive: Member variable 'PatternParams::fixName' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:538:2: warning: Member variable 'TabbedPatternSource::secondName_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:596:2: warning: Member variable 'FastaContinuousPatternSource::buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/pat.h:596:2: warning: Member variable 'FastaContinuousPatternSource::name_int_buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::patId' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::oms' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::fw' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::mfw' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::mlen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::cost' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::mate' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::primer' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:58:2: warning: Member variable 'Hit::seed' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/hit.h:92:7: warning: Member variable 'Hit::primer' is not assigned a value in 'Hit::operator='. [operatorEqVarError]
bowtie-1.3.1/hit.h:141:11: warning: Member variable 'HitSink::first_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_len' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_bwtLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_sz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_bwtSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_lineRate' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_linesPerSide' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_offRate' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_offMask' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_isaRate' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_isaMask' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_eftabLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_eftabSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_ftabLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_ftabSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_offsLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_offsSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_isaLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_isaSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_lineSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_sideSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_sideBwtSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_sideBwtLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_numSidePairs' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_numSides' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_numLines' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_ebwtTotLen' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_ebwtTotSz' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt.h:119:2: warning:inconclusive: Member variable 'EbwtParams::_isBt2Index' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/aligner_metrics.h:22:2: warning: Member variable 'RunningStat::m_oldM' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/aligner_metrics.h:22:2: warning: Member variable 'RunningStat::m_newM' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/aligner_metrics.h:22:2: warning: Member variable 'RunningStat::m_oldS' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/aligner_metrics.h:22:2: warning: Member variable 'RunningStat::m_newS' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::id_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::depth0_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::depth1_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::depth2_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::depth3_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::rdepth_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::len_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::cost_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::ham_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::ranges_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::rangesSz_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::top_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:520:2: warning: Member variable 'Branch::bot_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt_search_backtrack.h:28:2: warning: Member variable 'GreedyDFSRangeSource::_bailedOnBacktracks' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt_search_backtrack.h:28:2: warning: Member variable 'GreedyDFSRangeSource::_patid' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt_search_backtrack.h:28:2: warning: Member variable 'GreedyDFSRangeSource::_seed' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ebwt_search_backtrack.h:2939:2: warning: Member variable 'EbwtSeededRangeSourceDriver::generating_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_source.h:2040:2: warning: Member variable 'CostAwareRangeSourceDriver < EbwtRangeSource >::randSeed_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ls.h:43:1: style: The class 'LarssonSadakane < int >' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
bowtie-1.3.1/sstring.h:1622:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1622:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1633:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1633:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1658:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1658:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1670:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1670:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1682:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1682:11: warning: Member variable 'SStringExpandable < char , 25 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1622:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1622:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1633:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1633:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1658:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1658:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1670:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1670:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1682:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:1682:11: warning: Member variable 'SStringExpandable < char , 0 , 2 , 2048 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/sstring.h:586:14: warning: Member variable 'SString < char >::cs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
bowtie-1.3.1/sstring.h:586:14: warning: Member variable 'SString < char >::printcs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
bowtie-1.3.1/sstring.h:586:14: warning: Member variable 'SString < char >::len_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < Edit , 128 >::cat_' is not assigned a value in 'EList < Edit , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < HitSetEnt , 128 >::cat_' is not assigned a value in 'EList < HitSetEnt , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < FmStringOp , 128 >::cat_' is not assigned a value in 'EList < FmStringOp , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < Read , 128 >::cat_' is not assigned a value in 'EList < Read , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < bool , 128 >::cat_' is not assigned a value in 'EList < bool , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < PatternSource * , 128 >::cat_' is not assigned a value in 'EList < PatternSource * , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < PatternSourcePerThread * , 128 >::cat_' is not assigned a value in 'EList < PatternSourcePerThread * , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < uint32_t , 128 >::cat_' is not assigned a value in 'EList < uint32_t , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < char , 128 >::cat_' is not assigned a value in 'EList < char , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < Hit , 128 >::cat_' is not assigned a value in 'EList < Hit , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < SStringExpandable < char , 25 , 2 , 0 > , 128 >::cat_' is not assigned a value in 'EList < SStringExpandable < char , 25 , 2 , 0 > , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < unsigned long , 128 >::cat_' is not assigned a value in 'EList < unsigned long , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < PtBufInfo , 128 >::cat_' is not assigned a value in 'EList < PtBufInfo , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < FileBuf * , 128 >::cat_' is not assigned a value in 'EList < FileBuf * , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < RefRecord , 128 >::cat_' is not assigned a value in 'EList < RefRecord , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < SString < char > , 128 >::cat_' is not assigned a value in 'EList < SString < char > , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < uint8_t , 128 >::cat_' is not assigned a value in 'EList < uint8_t , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < union PartialAlignment , 128 >::cat_' is not assigned a value in 'EList < union PartialAlignment , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < QueryMutation , 128 >::cat_' is not assigned a value in 'EList < QueryMutation , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/bitset.h:264:10: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf]
bowtie-1.3.1/hit.h:595:9: style:inconclusive: Member variable 'HitSink::nthreads_' is in the wrong place in the initializer list. [initializerList]
bowtie-1.3.1/hit.h:161:3: note: Member variable 'HitSink::nthreads_' is in the wrong place in the initializer list.
bowtie-1.3.1/hit.h:595:9: note: Member variable 'HitSink::nthreads_' is in the wrong place in the initializer list.
bowtie-1.3.1/hit.h:601:7: style:inconclusive: Member variable 'HitSink::reorder_' is in the wrong place in the initializer list. [initializerList]
bowtie-1.3.1/hit.h:166:3: note: Member variable 'HitSink::reorder_' is in the wrong place in the initializer list.
bowtie-1.3.1/hit.h:601:7: note: Member variable 'HitSink::reorder_' is in the wrong place in the initializer list.
bowtie-1.3.1/hit.h:600:9: style:inconclusive: Member variable 'HitSink::next_batch_to_flush_' is in the wrong place in the initializer list. [initializerList]
bowtie-1.3.1/hit.h:167:3: note: Member variable 'HitSink::next_batch_to_flush_' is in the wrong place in the initializer list.
bowtie-1.3.1/hit.h:600:9: note: Member variable 'HitSink::next_batch_to_flush_' is in the wrong place in the initializer list.
bowtie-1.3.1/ref_read.h:31:3: performance: Variable 'msg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ebwt.h:498:3: performance: Variable '_in1Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/ebwt.h:499:3: performance: Variable '_in2Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie-1.3.1/bitset.h:85:7: style:inconclusive: Technically the member function 'SyncBitset::testUnsync' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1383:7: style:inconclusive: Technically the member function 'S2bDnaString::operator==' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1390:7: style:inconclusive: Technically the member function 'S2bDnaString::operator!=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1397:7: style:inconclusive: Technically the member function 'S2bDnaString::operator<' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1404:7: style:inconclusive: Technically the member function 'S2bDnaString::operator>' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1411:7: style:inconclusive: Technically the member function 'S2bDnaString::operator<=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1418:7: style:inconclusive: Technically the member function 'S2bDnaString::operator>=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:2391:7: style:inconclusive: Technically the member function 'SStringFixed::operator==' can be const. [functionConst]
bowtie-1.3.1/sstring.h:2398:7: style:inconclusive: Technically the member function 'SStringFixed::operator!=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:2405:7: style:inconclusive: Technically the member function 'SStringFixed::operator<' can be const. [functionConst]
bowtie-1.3.1/sstring.h:2412:7: style:inconclusive: Technically the member function 'SStringFixed::operator>' can be const. [functionConst]
bowtie-1.3.1/sstring.h:2419:7: style:inconclusive: Technically the member function 'SStringFixed::operator<=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:2426:7: style:inconclusive: Technically the member function 'SStringFixed::operator>=' can be const. [functionConst]
bowtie-1.3.1/filebuf.h:102:7: style:inconclusive: Technically the member function 'FileBuf::isOpen' can be const. [functionConst]
bowtie-1.3.1/filebuf.h:137:7: style:inconclusive: Technically the member function 'FileBuf::eof' can be const. [functionConst]
bowtie-1.3.1/filebuf.h:791:14: style:inconclusive: Technically the member function 'OutFileBuf::name' can be const. [functionConst]
bowtie-1.3.1/pat.h:418:7: performance:inconclusive: Technically the member function 'CFilePatternSource::is_gzipped_file' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/timer.h:111:7: style:inconclusive: Technically the member function 'Timer::write' can be const. [functionConst]
bowtie-1.3.1/hit.h:120:7: style:inconclusive: Technically the member function 'HitCostCompare::operator()' can be const. [functionConst]
bowtie-1.3.1/hit.h:629:17: performance:inconclusive: Technically the member function 'HitSink::openOf' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/hit.h:814:11: style:inconclusive: Technically the member function 'HitSinkPerThread::numValidHits' can be const. [functionConst]
bowtie-1.3.1/hit.h:852:11: style:inconclusive: Technically the member function 'HitSinkPerThread::overThresh' can be const. [functionConst]
bowtie-1.3.1/hit.h:856:7: style:inconclusive: Technically the member function 'HitSinkPerThread::exceededOverThresh' can be const. [functionConst]
bowtie-1.3.1/ebwt.h:575:7: style:inconclusive: Technically the member function 'Ebwt::isPacked' can be const. [functionConst]
bowtie-1.3.1/ebwt.h:825:13: performance:inconclusive: Technically the member function 'Ebwt::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ebwt.h:1251:11: performance:inconclusive: Technically the member function 'Ebwt::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ebwt.h:1500:7: style:inconclusive: Technically the member function 'SideLocus::valid' can be const. [functionConst]
bowtie-1.3.1/aligner_metrics.h:198:15: performance:inconclusive: Technically the member function 'AlignerMetrics::entropyDna5' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ebwt_search_util.h:303:9: style:inconclusive: Technically the member function 'PartialAlignmentManager::size' can be const. [functionConst]
bowtie-1.3.1/pool.h:71:11: style:inconclusive: Technically the member function 'ChunkPool::pos' can be const. [functionConst]
bowtie-1.3.1/range_source.h:796:7: style:inconclusive: Technically the member function 'Branch::print' can be const. [functionConst]
bowtie-1.3.1/range_source.h:1259:11: performance:inconclusive: Technically the member function 'BranchQueue::bestStratumAndHam' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/range_source.h:1378:11: style:inconclusive: Technically the member function 'PathManager::size' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:189:11: style:inconclusive: Technically the member function 'GreedyDFSRangeSource::numBacktracks' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:224:11: style:inconclusive: Technically the member function 'GreedyDFSRangeSource::maxBacktracks' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:1096:7: style:inconclusive: Technically the member function 'GreedyDFSRangeSource::printHit' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:1164:6: style:inconclusive: Technically the member function 'GreedyDFSRangeSource::calcStratum' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:1281:17: style:inconclusive: Technically the member function 'GreedyDFSRangeSource::qualAt' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:1286:20: performance:inconclusive: Technically the member function 'GreedyDFSRangeSource::pairTop' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ebwt_search_backtrack.h:1291:20: performance:inconclusive: Technically the member function 'GreedyDFSRangeSource::pairBot' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ebwt_search_backtrack.h:2444:7: style:inconclusive: Technically the member function 'EbwtRangeSource::hhCheckTop' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:2480:17: style:inconclusive: Technically the member function 'EbwtRangeSource::qualAt' can be const. [functionConst]
bowtie-1.3.1/ebwt_search_backtrack.h:2814:18: performance:inconclusive: Technically the member function 'EbwtRangeSourceDriver::cextToDepth' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/diff_sample.h:593:7: style:inconclusive: Technically the member function 'DifferenceCoverSample < S2bDnaString >::print' can be const. [functionConst]
bowtie-1.3.1/ls.h:187:14: performance:inconclusive: Technically the member function 'LarssonSadakane < int >::bucketsort' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/sstring.h:1864:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 25 , 2 , 0 >::operator==' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1871:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 25 , 2 , 0 >::operator!=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1878:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 25 , 2 , 0 >::operator<' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1885:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 25 , 2 , 0 >::operator>' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1892:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 25 , 2 , 0 >::operator<=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1899:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 25 , 2 , 0 >::operator>=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1864:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 0 , 2 , 2048 >::operator==' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1871:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 0 , 2 , 2048 >::operator!=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1878:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 0 , 2 , 2048 >::operator<' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1885:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 0 , 2 , 2048 >::operator>' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1892:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 0 , 2 , 2048 >::operator<=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:1899:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 0 , 2 , 2048 >::operator>=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:735:7: style:inconclusive: Technically the member function 'SString < char >::operator==' can be const. [functionConst]
bowtie-1.3.1/sstring.h:742:7: style:inconclusive: Technically the member function 'SString < char >::operator!=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:749:7: style:inconclusive: Technically the member function 'SString < char >::operator<' can be const. [functionConst]
bowtie-1.3.1/sstring.h:756:7: style:inconclusive: Technically the member function 'SString < char >::operator>' can be const. [functionConst]
bowtie-1.3.1/sstring.h:763:7: style:inconclusive: Technically the member function 'SString < char >::operator<=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:770:7: style:inconclusive: Technically the member function 'SString < char >::operator>=' can be const. [functionConst]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Edit , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Edit , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < HitSetEnt , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < HitSetEnt , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < FmStringOp , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < FmStringOp , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Read , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Read , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < bool , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < bool , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < PatternSource * , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < PatternSource * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < PatternSourcePerThread * , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < PatternSourcePerThread * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint32_t , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < uint32_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < char , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < char , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Hit , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Hit , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SStringExpandable < char , 25 , 2 , 0 > , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SStringExpandable < char , 25 , 2 , 0 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < unsigned long , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < unsigned long , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < PtBufInfo , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < PtBufInfo , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < FileBuf * , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < FileBuf * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < RefRecord , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < RefRecord , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SString < char > , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SString < char > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint8_t , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < uint8_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < union PartialAlignment , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:687:3: debug: CheckClass::isMemberVar found used member variable 'cur_' with varid 0 [varid0]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < union PartialAlignment , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:758:3: debug: CheckClass::isMemberVar found used member variable 'cur_' with varid 0 [varid0]
bowtie-1.3.1/ds.h:759:10: debug: CheckClass::isMemberVar found used member variable 'list_' with varid 0 [varid0]
bowtie-1.3.1/ds.h:857:32: debug: CheckClass::isMemberVar found used member variable 'list_' with varid 0 [varid0]
bowtie-1.3.1/ds.h:879:15: debug: CheckClass::isMemberVar found used member variable 'cur_' with varid 0 [varid0]
bowtie-1.3.1/ds.h:887:7: debug: CheckClass::isMemberVar found used member variable 'list_' with varid 0 [varid0]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < QueryMutation , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < QueryMutation , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/bitset.h:63:4: warning: Class 'SyncBitset' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/bitset.h:63:4: warning: Class 'SyncBitset' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/bitset.h:405:3: warning: Class 'FixedBitset2' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/bitset.h:405:3: warning: Class 'FixedBitset2' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/hit.h:170:3: warning: Class 'HitSink' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/hit.h:170:3: warning: Class 'HitSink' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/reference.h:251:6: warning: Class 'BitPairReference' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/reference.h:251:6: warning: Class 'BitPairReference' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/pool.h:38:8: warning: Class 'ChunkPool' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/pool.h:38:8: warning: Class 'ChunkPool' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/ds.h:116:3: warning: Class 'AutoArray < uint32_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/ds.h:116:3: warning: Class 'AutoArray < uint32_t >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/ds.h:116:3: warning: Class 'AutoArray < std :: thread * >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/ds.h:116:3: warning: Class 'AutoArray < std :: thread * >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/sstring.h:2353:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const std::basic_string<T>&str)' at line 2210. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2210:3: note: Calling install
bowtie-1.3.1/sstring.h:2353:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:2353:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b,long sz)' at line 2217. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2217:3: note: Calling install
bowtie-1.3.1/sstring.h:2353:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:2353:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b)' at line 2224. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2224:3: note: Calling install
bowtie-1.3.1/sstring.h:2353:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:2761:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2671. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2671:5: note: Calling installColors
bowtie-1.3.1/sstring.h:2761:15: note: installColors is a virtual function
bowtie-1.3.1/sstring.h:2746:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2673. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2673:5: note: Calling installChars
bowtie-1.3.1/sstring.h:2746:15: note: installChars is a virtual function
bowtie-1.3.1/sstring.h:2730:15: style: Virtual function 'install' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2676. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2676:4: note: Calling install
bowtie-1.3.1/sstring.h:2730:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:3317:15: style: Virtual function 'installChars' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3241. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:3241:4: note: Calling installChars
bowtie-1.3.1/sstring.h:3317:15: note: installChars is a virtual function
bowtie-1.3.1/sstring.h:3301:15: style: Virtual function 'install' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3243. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:3243:4: note: Calling install
bowtie-1.3.1/sstring.h:3301:15: note: install is a virtual function
bowtie-1.3.1/pat.h:641:15: style: Virtual function 'resetForNextFile' is called from constructor 'FastaContinuousPatternSource(const EList < string , 128 >&infiles,long length,long freq)' at line 614. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/pat.h:614:4: note: Calling resetForNextFile
bowtie-1.3.1/pat.h:641:15: note: resetForNextFile is a virtual function
bowtie-1.3.1/blockwise_sa.h:356:15: style: Virtual function 'reset' is called from constructor 'KarkkainenBlockwiseSA < S2bDnaString >(const S2bDnaString&__text,uint32_t __bucketSz,int __nthreads,uint32_t __dcV,uint32_t __seed=0,bool __sanityCheck=false,bool __passMemExc=false,bool __verbose=false,std::string base_fname="",ostream&__logger=cout)' at line 199. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/blockwise_sa.h:199:30: note: Calling reset
bowtie-1.3.1/blockwise_sa.h:356:15: note: reset is a virtual function
bowtie-1.3.1/sstring.h:3085:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable < 25 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2923. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2923:5: note: Calling installColors
bowtie-1.3.1/sstring.h:3085:15: note: installColors is a virtual function
bowtie-1.3.1/sstring.h:3077:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable < 25 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2925. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2925:5: note: Calling installChars
bowtie-1.3.1/sstring.h:3077:15: note: installChars is a virtual function
bowtie-1.3.1/sstring.h:3015:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 25 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2928. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2928:4: note: Calling install
bowtie-1.3.1/sstring.h:3015:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:3063:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable < 25 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2944. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2944:5: note: Calling installColors
bowtie-1.3.1/sstring.h:3063:15: note: installColors is a virtual function
bowtie-1.3.1/sstring.h:3049:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable < 25 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2946. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2946:5: note: Calling installChars
bowtie-1.3.1/sstring.h:3049:15: note: installChars is a virtual function
bowtie-1.3.1/sstring.h:3034:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 25 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2949. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2949:4: note: Calling install
bowtie-1.3.1/sstring.h:3034:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:3015:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 25 , 2 >(const char*b,bool chars=false,bool colors=false)' at line 2962. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:2962:3: note: Calling install
bowtie-1.3.1/sstring.h:3015:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:1825:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 25 , 2 , 0 >(const std::basic_string<char>&str)' at line 1664. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:1664:3: note: Calling install
bowtie-1.3.1/sstring.h:1825:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:1825:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 25 , 2 , 0 >(const char*b,long sz)' at line 1676. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:1676:3: note: Calling install
bowtie-1.3.1/sstring.h:1825:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:1825:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 25 , 2 , 0 >(const char*b)' at line 1688. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:1688:3: note: Calling install
bowtie-1.3.1/sstring.h:1825:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:1825:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 0 , 2 , 2048 >(const std::basic_string<char>&str)' at line 1664. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:1664:3: note: Calling install
bowtie-1.3.1/sstring.h:1825:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:1825:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 0 , 2 , 2048 >(const char*b,long sz)' at line 1676. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:1676:3: note: Calling install
bowtie-1.3.1/sstring.h:1825:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:1825:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 0 , 2 , 2048 >(const char*b)' at line 1688. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:1688:3: note: Calling install
bowtie-1.3.1/sstring.h:1825:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:687:15: style: Virtual function 'install' is called from constructor 'SString < char >(const std::basic_string<char>&str)' at line 543. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:543:3: note: Calling install
bowtie-1.3.1/sstring.h:687:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:687:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b,long sz)' at line 554. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:554:3: note: Calling install
bowtie-1.3.1/sstring.h:687:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:687:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b)' at line 565. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:565:3: note: Calling install
bowtie-1.3.1/sstring.h:687:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:2791:7: warning: The class 'SDnaStringFixed' defines member function with name 'set' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
bowtie-1.3.1/sstring.h:2325:7: note: Parent function 'SStringFixed::set'
bowtie-1.3.1/sstring.h:2791:7: note: Derived function 'SDnaStringFixed::set'
bowtie-1.3.1/sstring.h:2838:14: warning: The class 'SDnaStringFixed' defines member function with name 'operator[]' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
bowtie-1.3.1/sstring.h:2232:18: note: Parent function 'SStringFixed::operator[]'
bowtie-1.3.1/sstring.h:2838:14: note: Derived function 'SDnaStringFixed::operator[]'
bowtie-1.3.1/sstring.h:2845:14: warning: The class 'SDnaStringFixed' defines member function with name 'get' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
bowtie-1.3.1/sstring.h:2246:18: note: Parent function 'SStringFixed::get'
bowtie-1.3.1/sstring.h:2845:14: note: Derived function 'SDnaStringFixed::get'
bowtie-1.3.1/pat.h:516:7: warning: The class 'FastaPatternSource' defines member variable with name 'first_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie-1.3.1/pat.h:443:7: note: Parent variable 'CFilePatternSource::first_'
bowtie-1.3.1/pat.h:516:7: note: Derived variable 'FastaPatternSource::first_'
bowtie-1.3.1/pat.h:657:7: warning: The class 'FastaContinuousPatternSource' defines member variable with name 'buf_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie-1.3.1/pat.h:444:7: note: Parent variable 'CFilePatternSource::buf_'
bowtie-1.3.1/pat.h:657:7: note: Derived variable 'FastaContinuousPatternSource::buf_'
bowtie-1.3.1/pat.h:732:7: warning: The class 'FastqPatternSource' defines member variable with name 'first_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie-1.3.1/pat.h:443:7: note: Parent variable 'CFilePatternSource::first_'
bowtie-1.3.1/pat.h:732:7: note: Derived variable 'FastqPatternSource::first_'
bowtie-1.3.1/pat.h:794:7: warning: The class 'RawPatternSource' defines member variable with name 'first_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie-1.3.1/pat.h:443:7: note: Parent variable 'CFilePatternSource::first_'
bowtie-1.3.1/pat.h:794:7: note: Derived variable 'RawPatternSource::first_'
bowtie-1.3.1/range_source.h:1881:2: warning: The class 'SingleRangeSourceDriver < EbwtRangeSource >' defines member variable with name 'allTops_' also defined in its parent class 'RangeSourceDriver < EbwtRangeSource >'. [duplInheritedMember]
bowtie-1.3.1/range_source.h:1708:22: note: Parent variable 'RangeSourceDriver < EbwtRangeSource >::allTops_'
bowtie-1.3.1/range_source.h:1881:2: note: Derived variable 'SingleRangeSourceDriver < EbwtRangeSource >::allTops_'
bowtie-1.3.1/ebwt_search_backtrack.h:2830:19: warning: The class 'EbwtRangeSourceDriver' defines member variable with name 'rs_' also defined in its parent class 'SingleRangeSourceDriver < EbwtRangeSource >'. [duplInheritedMember]
bowtie-1.3.1/range_source.h:1878:34: note: Parent variable 'SingleRangeSourceDriver < EbwtRangeSource >::rs_'
bowtie-1.3.1/ebwt_search_backtrack.h:2830:19: note: Derived variable 'EbwtRangeSourceDriver::rs_'
bowtie-1.3.1/bitset.h:60:2: style: Class 'SyncBitset' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/bitset.h:166:2: style: Class 'Bitset' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/bitset.h:404:2: style: Class 'FixedBitset2' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/filebuf.h:70:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/filebuf.h:76:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/filebuf.h:82:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/filebuf.h:88:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/filebuf.h:537:2: style: Class 'BitpairOutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/filebuf.h:607:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/filebuf.h:622:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/hit_set.h:210:2: style: Struct 'HitSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/pat.h:94:2: style: Struct 'PerThreadReadBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/pat.h:243:2: style: Class 'TrimmingPatternSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/pat.h:262:2: style: Class 'VectorPatternSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/pat.h:674:2: style: Class 'FastqPatternSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/pat.h:748:2: style: Class 'RawPatternSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/pat.h:839:2: style: Class 'SoloPatternComposer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/timer.h:98:2: style: Class 'Timer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ebwt.h:328:2: style: Class 'EbwtFileOpenException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ebwt_search_util.h:170:2: style: Class 'PartialAlignmentManager' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/range_source.h:1945:2: style: Class 'ListRangeSourceDriver' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/row_chaser.h:25:2: style: Class 'RowChaser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/sstring.h:1645:2: style: Class 'SStringExpandable < char , 25 , 2 , 0 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/sstring.h:1645:2: style: Class 'SStringExpandable < char , 0 , 2 , 2048 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:114:2: style: Class 'AutoArray < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ds.h:114:2: style: Class 'AutoArray < std :: thread * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/sstring.h:2680:11: style: The destructor '~SDnaStringFixed' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/sstring.h:2227:11: note: Virtual destructor in base class
bowtie-1.3.1/sstring.h:2680:11: note: Destructor in derived class
bowtie-1.3.1/pat.h:267:11: style: The destructor '~VectorPatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:186:11: note: Virtual destructor in base class
bowtie-1.3.1/pat.h:267:11: note: Destructor in derived class
bowtie-1.3.1/pat.h:275:26: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:195:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:275:26: note: Function in derived class
bowtie-1.3.1/pat.h:283:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:206:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:283:15: note: Function in derived class
bowtie-1.3.1/pat.h:292:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:203:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:292:15: note: Function in derived class
bowtie-1.3.1/pat.h:345:11: style: The destructor '~CFilePatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:186:11: note: Virtual destructor in base class
bowtie-1.3.1/pat.h:345:11: note: Destructor in derived class
bowtie-1.3.1/pat.h:373:26: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:195:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:373:26: note: Function in derived class
bowtie-1.3.1/pat.h:382:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:206:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:382:15: note: Function in derived class
bowtie-1.3.1/pat.h:479:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:382:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:479:15: note: Function in derived class
bowtie-1.3.1/pat.h:487:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:203:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:487:15: note: Function in derived class
bowtie-1.3.1/pat.h:494:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:395:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:494:31: note: Function in derived class
bowtie-1.3.1/pat.h:502:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:403:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:502:15: note: Function in derived class
bowtie-1.3.1/pat.h:506:15: style: The function 'dump' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:219:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:506:15: note: Function in derived class
bowtie-1.3.1/pat.h:558:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:203:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:558:15: note: Function in derived class
bowtie-1.3.1/pat.h:565:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:395:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:565:31: note: Function in derived class
bowtie-1.3.1/pat.h:573:15: style: The function 'dump' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:219:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:573:15: note: Function in derived class
bowtie-1.3.1/pat.h:618:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:382:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:618:15: note: Function in derived class
bowtie-1.3.1/pat.h:626:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:203:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:626:15: note: Function in derived class
bowtie-1.3.1/pat.h:633:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:395:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:633:31: note: Function in derived class
bowtie-1.3.1/pat.h:641:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:403:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:641:15: note: Function in derived class
bowtie-1.3.1/pat.h:694:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:382:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:694:15: note: Function in derived class
bowtie-1.3.1/pat.h:702:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:203:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:702:15: note: Function in derived class
bowtie-1.3.1/pat.h:713:26: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:395:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:713:26: note: Function in derived class
bowtie-1.3.1/pat.h:718:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:403:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:718:15: note: Function in derived class
bowtie-1.3.1/pat.h:722:15: style: The function 'dump' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:219:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:722:15: note: Function in derived class
bowtie-1.3.1/pat.h:759:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:382:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:759:15: note: Function in derived class
bowtie-1.3.1/pat.h:767:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:203:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:767:15: note: Function in derived class
bowtie-1.3.1/pat.h:774:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:395:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:774:31: note: Function in derived class
bowtie-1.3.1/pat.h:779:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:403:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:779:15: note: Function in derived class
bowtie-1.3.1/pat.h:783:15: style: The function 'dump' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:219:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:783:15: note: Function in derived class
bowtie-1.3.1/pat.h:853:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:807:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:853:15: note: Function in derived class
bowtie-1.3.1/pat.h:865:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:812:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:865:18: note: Function in derived class
bowtie-1.3.1/pat.h:870:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:817:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:870:15: note: Function in derived class
bowtie-1.3.1/pat.h:912:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:807:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:912:15: note: Function in derived class
bowtie-1.3.1/pat.h:927:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:812:31: note: Virtual function in base class
bowtie-1.3.1/pat.h:927:18: note: Function in derived class
bowtie-1.3.1/pat.h:932:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/pat.h:817:15: note: Virtual function in base class
bowtie-1.3.1/pat.h:932:15: note: Function in derived class
bowtie-1.3.1/hit.h:949:15: style: The function 'spanStrata' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:859:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:949:15: note: Function in derived class
bowtie-1.3.1/hit.h:953:15: style: The function 'best' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:862:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:953:15: note: Function in derived class
bowtie-1.3.1/hit.h:958:19: style: The function 'finishReadImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:788:19: note: Virtual function in base class
bowtie-1.3.1/hit.h:958:19: note: Function in derived class
bowtie-1.3.1/hit.h:969:15: style: The function 'reportHit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:807:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:969:15: note: Function in derived class
bowtie-1.3.1/hit.h:991:15: style: The function 'finishedWithStratumImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:849:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:991:15: note: Function in derived class
bowtie-1.3.1/hit.h:1015:28: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:921:28: note: Virtual function in base class
bowtie-1.3.1/hit.h:1015:28: note: Function in derived class
bowtie-1.3.1/hit.h:1019:28: style: The function 'createMult' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:922:28: note: Virtual function in base class
bowtie-1.3.1/hit.h:1019:28: note: Function in derived class
bowtie-1.3.1/hit.h:1056:15: style: The function 'spanStrata' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:859:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1056:15: note: Function in derived class
bowtie-1.3.1/hit.h:1063:15: style: The function 'best' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:862:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1063:15: note: Function in derived class
bowtie-1.3.1/hit.h:1070:15: style: The function 'reportHit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:807:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1070:15: note: Function in derived class
bowtie-1.3.1/hit.h:1098:19: style: The function 'finishReadImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:788:19: note: Virtual function in base class
bowtie-1.3.1/hit.h:1098:19: note: Function in derived class
bowtie-1.3.1/hit.h:1115:15: style: The function 'finishedWithStratumImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:849:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1115:15: note: Function in derived class
bowtie-1.3.1/hit.h:1123:15: style: The function 'irrelevantCost' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:840:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1123:15: note: Function in derived class
bowtie-1.3.1/hit.h:1158:28: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:921:28: note: Virtual function in base class
bowtie-1.3.1/hit.h:1158:28: note: Function in derived class
bowtie-1.3.1/hit.h:1162:28: style: The function 'createMult' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:922:28: note: Virtual function in base class
bowtie-1.3.1/hit.h:1162:28: note: Function in derived class
bowtie-1.3.1/hit.h:1189:15: style: The function 'spanStrata' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:859:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1189:15: note: Function in derived class
bowtie-1.3.1/hit.h:1193:15: style: The function 'best' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:862:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1193:15: note: Function in derived class
bowtie-1.3.1/hit.h:1201:15: style: The function 'reportHit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:807:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1201:15: note: Function in derived class
bowtie-1.3.1/hit.h:1214:19: style: The function 'finishReadImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:788:19: note: Virtual function in base class
bowtie-1.3.1/hit.h:1214:19: note: Function in derived class
bowtie-1.3.1/hit.h:1223:15: style: The function 'finishedWithStratumImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:849:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1223:15: note: Function in derived class
bowtie-1.3.1/hit.h:1245:28: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:921:28: note: Virtual function in base class
bowtie-1.3.1/hit.h:1245:28: note: Function in derived class
bowtie-1.3.1/hit.h:1248:28: style: The function 'createMult' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:922:28: note: Virtual function in base class
bowtie-1.3.1/hit.h:1248:28: note: Function in derived class
bowtie-1.3.1/hit.h:1336:15: style: The function 'append' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:206:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1336:15: note: Function in derived class
bowtie-1.3.1/hit.h:1344:15: style: The function 'reportMaxed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:494:15: note: Virtual function in base class
bowtie-1.3.1/hit.h:1344:15: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:1831:15: style: The function 'setQuery' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1590:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:1831:15: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:1900:17: style: The function 'range' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1597:17: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:1900:17: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:1921:2: style: The function 'initBranch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1592:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:1921:2: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:2060:2: style: The function 'advanceBranch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1594:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:2060:2: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:2710:11: style: The destructor '~EbwtRangeSourceDriver' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1743:11: note: Virtual destructor in base class
bowtie-1.3.1/ebwt_search_backtrack.h:2710:11: note: Destructor in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:2955:11: style: The destructor '~EbwtSeededRangeSourceDriver' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1622:11: note: Virtual destructor in base class
bowtie-1.3.1/ebwt_search_backtrack.h:2955:11: note: Destructor in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:2963:15: style: The function 'setQueryImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1636:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:2963:15: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:2984:15: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1642:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:2984:15: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:3011:15: style: The function 'advanceImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1662:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:3011:15: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:3108:17: style: The function 'range' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1666:17: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:3108:17: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:3119:15: style: The function 'mate1' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1672:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:3119:15: note: Function in derived class
bowtie-1.3.1/ebwt_search_backtrack.h:3126:15: style: The function 'fw' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1677:15: note: Virtual function in base class
bowtie-1.3.1/ebwt_search_backtrack.h:3126:15: note: Function in derived class
bowtie-1.3.1/range_source.h:2066:11: style: The destructor '~CostAwareRangeSourceDriver < EbwtRangeSource >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1622:11: note: Virtual destructor in base class
bowtie-1.3.1/range_source.h:2066:11: note: Destructor in derived class
bowtie-1.3.1/range_source.h:2076:15: style: The function 'setQueryImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1636:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:2076:15: note: Function in derived class
bowtie-1.3.1/range_source.h:2144:15: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1642:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:2144:15: note: Function in derived class
bowtie-1.3.1/range_source.h:2157:15: style: The function 'advanceImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1662:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:2157:15: note: Function in derived class
bowtie-1.3.1/range_source.h:2213:17: style: The function 'range' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1666:17: note: Virtual function in base class
bowtie-1.3.1/range_source.h:2213:17: note: Function in derived class
bowtie-1.3.1/range_source.h:2222:15: style: The function 'mate1' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1672:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:2222:15: note: Function in derived class
bowtie-1.3.1/range_source.h:2229:15: style: The function 'fw' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1677:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:2229:15: note: Function in derived class
bowtie-1.3.1/range_source.h:2233:15: style: The function 'removeMate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1679:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:2233:15: note: Function in derived class
bowtie-1.3.1/range_source.h:1743:11: style: The destructor '~SingleRangeSourceDriver < EbwtRangeSource >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1622:11: note: Virtual destructor in base class
bowtie-1.3.1/range_source.h:1743:11: note: Destructor in derived class
bowtie-1.3.1/range_source.h:1750:15: style: The function 'setQueryImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1636:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1750:15: note: Function in derived class
bowtie-1.3.1/range_source.h:1777:15: style: The function 'advanceImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1662:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1777:15: note: Function in derived class
bowtie-1.3.1/range_source.h:1843:17: style: The function 'range' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1666:17: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1843:17: note: Function in derived class
bowtie-1.3.1/range_source.h:1853:7: style: The function 'mate1' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1672:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1853:7: note: Function in derived class
bowtie-1.3.1/range_source.h:1860:7: style: The function 'fw' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1677:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1860:7: note: Function in derived class
bowtie-1.3.1/blockwise_sa.h:201:3: style: The destructor '~KarkkainenBlockwiseSA < S2bDnaString >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/blockwise_sa.h:74:11: note: Virtual destructor in base class
bowtie-1.3.1/blockwise_sa.h:201:3: note: Destructor in derived class
bowtie-1.3.1/blockwise_sa.h:272:21: style: The function 'nextSuffix' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/blockwise_sa.h:83:21: note: Virtual function in base class
bowtie-1.3.1/blockwise_sa.h:272:21: note: Function in derived class
bowtie-1.3.1/blockwise_sa.h:335:15: style: The function 'nextBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/blockwise_sa.h:139:15: note: Virtual function in base class
bowtie-1.3.1/blockwise_sa.h:335:15: note: Function in derived class
bowtie-1.3.1/blockwise_sa.h:341:15: style: The function 'hasMoreBlocks' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/blockwise_sa.h:141:15: note: Virtual function in base class
bowtie-1.3.1/blockwise_sa.h:341:15: note: Function in derived class
bowtie-1.3.1/blockwise_sa.h:356:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/blockwise_sa.h:131:15: note: Virtual function in base class
bowtie-1.3.1/blockwise_sa.h:356:15: note: Function in derived class
bowtie-1.3.1/blockwise_sa.h:365:15: style: The function 'isReset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/blockwise_sa.h:133:15: note: Virtual function in base class
bowtie-1.3.1/blockwise_sa.h:365:15: note: Function in derived class
bowtie-1.3.1/sequence_io.h:130:17: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
bowtie-1.3.1/sequence_io.h:128:53: note: outer condition: baseCutoff>0
bowtie-1.3.1/sequence_io.h:130:17: note: opposite inner condition: baseCutoff<=0
bowtie-1.3.1/bowtie_inspect.cpp:381:5: style: The if condition is the same as the previous if condition [duplicateCondition]
bowtie-1.3.1/bowtie_inspect.cpp:377:5: note: First condition
bowtie-1.3.1/bowtie_inspect.cpp:381:5: note: Second condition
bowtie-1.3.1/qual.h:99:10: style: Condition 'cc<33' is always false [knownConditionTrueFalse]
bowtie-1.3.1/qual.h:98:40: note: Assignment 'cc=solexaToPhred((int)c-64)+33', assigned value is greater than 32
bowtie-1.3.1/qual.h:99:10: note: Condition 'cc<33' is always false
bowtie-1.3.1/diff_sample.h:220:13: style: Condition 'keepGoing' is always false [knownConditionTrueFalse]
bowtie-1.3.1/diff_sample.h:191:22: note: Assignment 'keepGoing=false', assigned value is 0
bowtie-1.3.1/diff_sample.h:220:13: note: Condition 'keepGoing' is always false
bowtie-1.3.1/reference.h:163:28: style: Condition 'willBeInEbwt' is always true [knownConditionTrueFalse]
bowtie-1.3.1/reference.h:162:25: note: Assignment 'willBeInEbwt=true', assigned value is 1
bowtie-1.3.1/reference.h:163:28: note: Condition 'willBeInEbwt' is always true
bowtie-1.3.1/reference.h:464:15: style: Condition 'count>0' is always true [knownConditionTrueFalse]
bowtie-1.3.1/reference.h:459:13: note: Assuming that condition 'count==0' is not redundant
bowtie-1.3.1/reference.h:464:15: note: Condition 'count>0' is always true
bowtie-1.3.1/reference.h:629:15: style: Condition 'count>0' is always true [knownConditionTrueFalse]
bowtie-1.3.1/reference.h:623:13: note: Assuming that condition 'count==0' is not redundant
bowtie-1.3.1/reference.h:629:15: note: Condition 'count>0' is always true
bowtie-1.3.1/range_source.h:991:47: style: Condition 'qs[0]<=qAllow' is always true [knownConditionTrueFalse]
bowtie-1.3.1/range_source.h:985:12: note: Assuming that condition 'qs[0]>qAllow' is not redundant
bowtie-1.3.1/range_source.h:991:47: note: Condition 'qs[0]<=qAllow' is always true
bowtie-1.3.1/range_source.h:994:7: style: Condition 'doInserts' is always false [knownConditionTrueFalse]
bowtie-1.3.1/range_source.h:988:20: note: Assignment 'doInserts=false', assigned value is 0
bowtie-1.3.1/range_source.h:994:7: note: Condition 'doInserts' is always false
bowtie-1.3.1/range_source.h:995:7: style: Condition 'doDeletes' is always false [knownConditionTrueFalse]
bowtie-1.3.1/range_source.h:989:20: note: Assignment 'doDeletes=false', assigned value is 0
bowtie-1.3.1/range_source.h:995:7: note: Condition 'doDeletes' is always false
bowtie-1.3.1/range_source.h:1002:7: style: Condition 'doInserts' is always false [knownConditionTrueFalse]
bowtie-1.3.1/range_source.h:988:20: note: Assignment 'doInserts=false', assigned value is 0
bowtie-1.3.1/range_source.h:1002:7: note: Condition 'doInserts' is always false
bowtie-1.3.1/range_source.h:1003:7: style: Condition 'doDeletes' is always false [knownConditionTrueFalse]
bowtie-1.3.1/range_source.h:989:20: note: Assignment 'doDeletes=false', assigned value is 0
bowtie-1.3.1/range_source.h:1003:7: note: Condition 'doDeletes' is always false
bowtie-1.3.1/range_source.h:1010:7: style: Condition 'doInserts' is always false [knownConditionTrueFalse]
bowtie-1.3.1/range_source.h:988:20: note: Assignment 'doInserts=false', assigned value is 0
bowtie-1.3.1/range_source.h:1010:7: note: Condition 'doInserts' is always false
bowtie-1.3.1/range_source.h:1476:8: style: Condition 'f->delayedIncrease_' is always true [knownConditionTrueFalse]
bowtie-1.3.1/range_source.h:1474:10: note: Assuming that condition 'f->delayedIncrease_' is not redundant
bowtie-1.3.1/range_source.h:1476:8: note: Condition 'f->delayedIncrease_' is always true
bowtie-1.3.1/ebwt_search_backtrack.h:267:31: style: Condition 'nsInFtab>0' is always false [knownConditionTrueFalse]
bowtie-1.3.1/ebwt_search_backtrack.h:254:15: note: Assuming that condition 'nsInFtab==0' is not redundant
bowtie-1.3.1/ebwt_search_backtrack.h:267:31: note: Condition 'nsInFtab>0' is always false
bowtie-1.3.1/ebwt_search_backtrack.h:278:30: style: Condition 'nsInFtab>0' is always false [knownConditionTrueFalse]
bowtie-1.3.1/ebwt_search_backtrack.h:254:15: note: Assuming that condition 'nsInFtab==0' is not redundant
bowtie-1.3.1/ebwt_search_backtrack.h:278:30: note: Condition 'nsInFtab>0' is always false
bowtie-1.3.1/ebwt.h:2048:30: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:2047:30: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2044:73: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2048:30: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie-1.3.1/ebwt.h:2103:30: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:2102:30: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2099:63: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2103:30: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie-1.3.1/ebwt.h:2151:30: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:2150:30: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2147:73: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2151:30: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie-1.3.1/ebwt.h:2200:30: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:2199:30: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2196:63: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2200:30: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie-1.3.1/ebwt.h:2251:30: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:2250:30: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2247:73: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2251:30: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie-1.3.1/ebwt.h:2304:30: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:2303:30: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2300:63: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie-1.3.1/ebwt.h:2304:30: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie-1.3.1/ebwt.h:2801:7: style: Condition 'mirror' is always false [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:2793:5: note: Assuming that condition 'mirror' is not redundant
bowtie-1.3.1/ebwt.h:2801:7: note: Condition 'mirror' is always false
bowtie-1.3.1/ebwt.h:3124:33: style: Condition 'shmemLeader' is always false [knownConditionTrueFalse]
bowtie-1.3.1/ebwt.h:3120:18: note: Assignment 'shmemLeader=0', assigned value is 0
bowtie-1.3.1/ebwt.h:3124:33: note: Condition 'shmemLeader' is always false
bowtie-1.3.1/ebwt.h:681:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt.h:1649:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt.h:3062:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt.h:3873:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt.h:4031:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt.h:4052:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt.h:4068:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt.h:4343:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/blockwise_sa.h:575:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/blockwise_sa.h:634:6: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/blockwise_sa.h:975:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/blockwise_sa.h:996:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/blockwise_sa.h:1042:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/blockwise_sa.h:1092:8: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/filebuf.h:643:18: error: Exception thrown in function declared not to throw exceptions. [throwInNoexceptFunction]
bowtie-1.3.1/reference.h:75:4: error: Resource leak: f3 [resourceLeak]
bowtie-1.3.1/reference.h:117:5: error: Resource leak: f4 [resourceLeak]
bowtie-1.3.1/reference.h:128:4: error: Resource leak: f4 [resourceLeak]
bowtie-1.3.1/filebuf.h:589:11: style: Class 'BitpairOutFileBuf' is unsafe, 'BitpairOutFileBuf::out_' can leak by wrong usage. [unsafeClassCanLeak]
bowtie-1.3.1/range_source.h:722:12: warning: Either the condition 'ranges_!=NULL' is redundant or there is possible null pointer dereference: ranges_. [nullPointerRedundantCheck]
bowtie-1.3.1/range_source.h:754:15: note: Assuming that condition 'ranges_!=NULL' is not redundant
bowtie-1.3.1/range_source.h:722:12: note: Null pointer dereference
bowtie-1.3.1/ebwt_search_backtrack.h:111:12: warning: Either the condition '_elims!=NULL' is redundant or there is possible null pointer dereference: _elims. [nullPointerRedundantCheck]
bowtie-1.3.1/ebwt_search_backtrack.h:115:37: note: Assuming that condition '_elims!=NULL' is not redundant
bowtie-1.3.1/ebwt_search_backtrack.h:111:12: note: Null pointer dereference
bowtie-1.3.1/endian_swap.h:22:11: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/sstring.h:90:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/filebuf.h:231:17: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/filebuf.h:234:29: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/filebuf.h:236:17: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/filebuf.h:560:17: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/filebuf.h:580:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/filebuf.h:771:22: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/edit.h:43:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/edit.h:50:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:35:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:36:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:43:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:44:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:46:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:49:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:56:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:57:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:63:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:65:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:67:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:73:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:221:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:226:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:232:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:243:13: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:252:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/hit_set.h:261:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/diff_sample.h:792:38: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:28:13: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:48:13: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:54:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:92:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/reference.h:359:23: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/reference.h:428:19: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/reference.h:487:19: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/reference.h:491:22: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/reference.h:566:10: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:1484:23: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/pool.h:100:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/pool.h:117:29: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search_backtrack.h:410:24: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search_backtrack.h:2192:42: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search_backtrack.h:2192:65: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search_backtrack.h:2203:28: style: C-style reference casting [cstyleCast]
bowtie-1.3.1/ebwt.h:1918:32: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:1987:17: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/row_chaser.h:135:38: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3053:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3098:15: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3138:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3141:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3211:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3235:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3260:7: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3308:17: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3321:27: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3344:19: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3347:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3396:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3415:15: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:3644:15: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:4260:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt.h:4280:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/bowtie_inspect.cpp:204:18: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/pool.h:339:15: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/pool.h:358:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/blockwise_sa.h:237:46: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/blockwise_sa.h:286:59: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/blockwise_sa.h:452:19: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/blockwise_sa.h:647:32: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/blockwise_sa.h:650:64: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:110:11: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:73:11: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:39:13: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/word_io.h:19:13: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/diff_sample.h:858:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/diff_sample.h:861:33: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/diff_sample.h:913:61: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/diff_sample.h:974:4: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/diff_sample.h:975:4: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/blockwise_sa.h:505:36: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search_backtrack.h:2726:12: style: Same expression used in consecutive assignments of 'sLeft' and 'sRight'. [duplicateAssignExpression]
bowtie-1.3.1/ebwt_search_backtrack.h:2727:12: note: Same expression used in consecutive assignments of 'sLeft' and 'sRight'.
bowtie-1.3.1/ebwt_search_backtrack.h:2726:12: note: Same expression used in consecutive assignments of 'sLeft' and 'sRight'.
bowtie-1.3.1/ebwt.h:3482:25: style: Same expression on both sides of '||'. [duplicateExpression]
bowtie-1.3.1/ebwt.h:3515:11: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie-1.3.1/ebwt.h:3511:10: note: c is initialized
bowtie-1.3.1/ebwt.h:3515:11: note: c is overwritten
bowtie-1.3.1/bowtie_inspect.cpp:103:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bowtie-1.3.1/ebwt_search_backtrack.h:757:5: style: The scope of the variable 'eligiblesVisited' can be reduced. [variableScope]
bowtie-1.3.1/ebwt_search_backtrack.h:1014:12: style: The scope of the variable 'kCurOverridesEligible' can be reduced. [variableScope]
bowtie-1.3.1/ebwt_search_backtrack.h:2726:12: style: The scope of the variable 'sLeft' can be reduced. [variableScope]
bowtie-1.3.1/ebwt.h:2590:14: style: The scope of the variable 'fraglen' can be reduced. [variableScope]
bowtie-1.3.1/bowtie_inspect.cpp:475:10: style: The scope of the variable 'outfile' can be reduced. [variableScope]
bowtie-1.3.1/bowtie_inspect.cpp:287:13: style: The scope of the variable 'tlen' can be reduced. [variableScope]
bowtie-1.3.1/blockwise_sa.h:956:13: style: The scope of the variable 'lo' can be reduced. [variableScope]
bowtie-1.3.1/blockwise_sa.h:1058:11: style: The scope of the variable 'kHi' can be reduced. [variableScope]
bowtie-1.3.1/blockwise_sa.h:1058:21: style: The scope of the variable 'kLo' can be reduced. [variableScope]
bowtie-1.3.1/blockwise_sa.h:1059:11: style: The scope of the variable 'jHi' can be reduced. [variableScope]
bowtie-1.3.1/blockwise_sa.h:1059:21: style: The scope of the variable 'jLo' can be reduced. [variableScope]
bowtie-1.3.1/blockwise_sa.h:1060:8: style: The scope of the variable 'kHiSoft' can be reduced. [variableScope]
bowtie-1.3.1/blockwise_sa.h:1060:25: style: The scope of the variable 'kLoSoft' can be reduced. [variableScope]
bowtie-1.3.1/diff_sample.h:843:13: style: The scope of the variable 'nextRank' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:101:8: style: The scope of the variable 'pl' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:101:18: style: The scope of the variable 'pn' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:102:7: style: The scope of the variable 's' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:128:7: style: The scope of the variable 'f' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:189:18: style: The scope of the variable 'd' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:189:21: style: The scope of the variable 'g' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:288:8: style: The scope of the variable 'pi' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:289:10: style: The scope of the variable 'j' can be reduced. [variableScope]
bowtie-1.3.1/ls.h:289:16: style: The scope of the variable 'sl' can be reduced. [variableScope]
bowtie-1.3.1/multikey_qsort.h:919:2: style: Unsigned expression 'lim' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ebwt_search_backtrack.h:993:5: style: Unsigned expression 'eligibleNum' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ebwt_search_backtrack.h:995:5: style: Unsigned expression 'altNum' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ebwt.h:1667:3: style: Unsigned expression 'this->_plen[i]' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/diff_sample.h:718:3: style: Unsigned expression 'sz' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/sstring.h:3468:46: warning: Either the condition '(poss)>(0)' is redundant or there is division by zero at line 3468. [zerodivcond]
bowtie-1.3.1/sstring.h:3467:3: note: Assuming that condition '(poss)>(0)' is not redundant
bowtie-1.3.1/sstring.h:3468:46: note: Division by zero
bowtie-1.3.1/bitpack.h:20:17: error: Shifting by a negative value is undefined behaviour [shiftNegative]
bowtie-1.3.1/filebuf.h:554:21: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
bowtie-1.3.1/ebwt.h:1963:63: style:inconclusive: Function 'countUpToEx' argument 2 names different: declaration 'pairs' definition 'arrs'. [funcArgNamesDifferent]
bowtie-1.3.1/ebwt.h:1148:58: note: Function 'countUpToEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:1963:63: note: Function 'countUpToEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2081:65: style:inconclusive: Function 'countFwSideEx' argument 2 names different: declaration 'pairs' definition 'arrs'. [funcArgNamesDifferent]
bowtie-1.3.1/ebwt.h:1150:60: note: Function 'countFwSideEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2081:65: note: Function 'countFwSideEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2184:65: style:inconclusive: Function 'countBwSideEx' argument 2 names different: declaration 'pairs' definition 'arrs'. [funcArgNamesDifferent]
bowtie-1.3.1/ebwt.h:1152:60: note: Function 'countBwSideEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2184:65: note: Function 'countBwSideEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2296:66: style:inconclusive: Function 'countBt2SideEx' argument 2 names different: declaration 'pairs' definition 'arrs'. [funcArgNamesDifferent]
bowtie-1.3.1/ebwt.h:1154:61: note: Function 'countBt2SideEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2296:66: note: Function 'countBt2SideEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2388:15: style:inconclusive: Function 'mapLFEx' argument 2 names different: declaration 'pairs' definition 'arrs'. [funcArgNamesDifferent]
bowtie-1.3.1/ebwt.h:1156:54: note: Function 'mapLFEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2388:15: note: Function 'mapLFEx' argument 2 names different: declaration 'pairs' definition 'arrs'.
bowtie-1.3.1/ebwt.h:2836:6: style:inconclusive: Function 'readIntoMemory' argument 1 names different: declaration 'needEntireReverse' definition 'needEntireRev'. [funcArgNamesDifferent]
bowtie-1.3.1/ebwt.h:1130:26: note: Function 'readIntoMemory' argument 1 names different: declaration 'needEntireReverse' definition 'needEntireRev'.
bowtie-1.3.1/ebwt.h:2836:6: note: Function 'readIntoMemory' argument 1 names different: declaration 'needEntireReverse' definition 'needEntireRev'.
bowtie-1.3.1/hit_set.h:233:29: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/hit_set.h:219:12: note: Shadowed declaration
bowtie-1.3.1/hit_set.h:233:29: note: Shadow variable
bowtie-1.3.1/sequence_io.h:95:15: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/sequence_io.h:71:14: note: Shadowed declaration
bowtie-1.3.1/sequence_io.h:95:15: note: Shadow variable
bowtie-1.3.1/sequence_io.h:103:14: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/sequence_io.h:71:14: note: Shadowed declaration
bowtie-1.3.1/sequence_io.h:103:14: note: Shadow variable
bowtie-1.3.1/diff_sample.h:235:8: style: Local variable 'i' shadows outer argument [shadowArgument]
bowtie-1.3.1/diff_sample.h:127:25: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:235:8: note: Shadow variable
bowtie-1.3.1/diff_sample.h:286:10: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/diff_sample.h:257:5: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:286:10: note: Shadow variable
bowtie-1.3.1/diff_sample.h:297:10: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/diff_sample.h:257:5: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:297:10: note: Shadow variable
bowtie-1.3.1/reference.h:112:8: style: Local variable 'swap' shadows outer function [shadowFunction]
bowtie-1.3.1/multikey_qsort.h:20:20: note: Shadowed declaration
bowtie-1.3.1/reference.h:112:8: note: Shadow variable
bowtie-1.3.1/reference.h:265:11: style: Local variable 'f4' shadows outer variable [shadowVariable]
bowtie-1.3.1/reference.h:63:14: note: Shadowed declaration
bowtie-1.3.1/reference.h:265:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:768:26: style: Local variable 'extra' shadows outer variable [shadowVariable]
bowtie-1.3.1/bowtie_inspect.cpp:20:13: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:768:26: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:695:16: style: Local variable 'd' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search_backtrack.h:454:12: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:695:16: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:899:18: style: Local variable 'j' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search_backtrack.h:758:19: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:899:18: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:921:14: style: Local variable 'j' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search_backtrack.h:758:19: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:921:14: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:1140:14: style: Local variable 'depth' shadows outer argument [shadowArgument]
bowtie-1.3.1/ebwt_search_backtrack.h:1118:45: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:1140:14: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:1248:17: style: Local variable 'd' shadows outer argument [shadowArgument]
bowtie-1.3.1/ebwt_search_backtrack.h:1201:27: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:1248:17: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:2417:14: style: Local variable 'depth' shadows outer argument [shadowArgument]
bowtie-1.3.1/ebwt_search_backtrack.h:2397:35: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:2417:14: note: Shadow variable
bowtie-1.3.1/ebwt.h:1588:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:866:20: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:1588:20: note: Shadow variable
bowtie-1.3.1/ebwt.h:1589:7: style: Local variable 'fw' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:884:14: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:1589:7: note: Shadow variable
bowtie-1.3.1/ebwt.h:1632:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:866:20: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:1632:20: note: Shadow variable
bowtie-1.3.1/ebwt.h:2717:20: style: Local variable 'offs' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:875:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2717:20: note: Shadow variable
bowtie-1.3.1/ebwt.h:2977:14: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:866:20: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2977:14: note: Shadow variable
bowtie-1.3.1/ebwt.h:3118:8: style: Local variable 'shmemLeader' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt.h:3066:7: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3118:8: note: Shadow variable
bowtie-1.3.1/ebwt.h:3344:12: style: Local variable 'offs' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:875:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3344:12: note: Shadow variable
bowtie-1.3.1/ebwt.h:3606:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:866:20: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3606:20: note: Shadow variable
bowtie-1.3.1/ebwt.h:3991:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:866:20: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3991:20: note: Shadow variable
bowtie-1.3.1/ebwt.h:4004:13: style: Local variable 'fchr' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:872:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:4004:13: note: Shadow variable
bowtie-1.3.1/ebwt.h:4005:20: style: Local variable 'ftab' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:873:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:4005:20: note: Shadow variable
bowtie-1.3.1/ebwt.h:4006:13: style: Local variable 'zOff' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:867:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:4006:13: note: Shadow variable
bowtie-1.3.1/ebwt.h:4085:7: style: Local variable 'fw' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:884:14: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:4085:7: note: Shadow variable
bowtie-1.3.1/ebwt.h:4335:20: style: Local variable 'eftab' shadows outer function [shadowFunction]
bowtie-1.3.1/ebwt.h:874:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:4335:20: note: Shadow variable
bowtie-1.3.1/ebwt.h:4375:15: style: Local variable 's' shadows outer argument [shadowArgument]
bowtie-1.3.1/ebwt.h:3987:22: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:4375:15: note: Shadow variable
bowtie-1.3.1/blockwise_sa.h:602:10: style: Local variable 'timer' shadows outer variable [shadowVariable]
bowtie-1.3.1/blockwise_sa.h:590:9: note: Shadowed declaration
bowtie-1.3.1/blockwise_sa.h:602:10: note: Shadow variable
bowtie-1.3.1/diff_sample.h:666:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:570:11: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:666:11: note: Shadow variable
bowtie-1.3.1/diff_sample.h:674:12: style: Local variable 'd' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:575:11: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:674:12: note: Shadow variable
bowtie-1.3.1/diff_sample.h:703:25: style: Local variable 'ds' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:579:25: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:703:25: note: Shadow variable
bowtie-1.3.1/diff_sample.h:705:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:570:11: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:705:11: note: Shadow variable
bowtie-1.3.1/diff_sample.h:706:11: style: Local variable 'd' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:575:11: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:706:11: note: Shadow variable
bowtie-1.3.1/diff_sample.h:833:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:570:11: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:833:11: note: Shadow variable
bowtie-1.3.1/diff_sample.h:1072:25: style: Local variable 'dmap' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:580:25: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:1072:25: note: Shadow variable
bowtie-1.3.1/diff_sample.h:1078:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie-1.3.1/diff_sample.h:570:11: note: Shadowed declaration
bowtie-1.3.1/diff_sample.h:1078:11: note: Shadow variable
bowtie-1.3.1/bitset.h:33:26: style: Variable 'ba' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/bitset.h:64:27: style: Variable 'ba' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/bitset.h:170:27: style: Variable 'ba' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/reference.h:253:29: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:825:41: style: Parameter 'szs' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/ebwt.h:1043:32: style: Parameter 'eh' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/range_source.h:1259:48: style: Parameter 'bset' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/ebwt.h:1647:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:3059:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:3129:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:3249:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:3286:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:3384:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:3870:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:4027:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:4048:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:4064:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:4339:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/bowtie_inspect.cpp:190:20: style: Parameter 'ref' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/bowtie_inspect.cpp:338:63: style: Parameter 'fout' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/bowtie_inspect.cpp:354:11: style: Parameter 'fout' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/bowtie_inspect.cpp:520:26: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/range_source.h:1723:12: style: Parameter 'sink' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/range_source.h:1725:24: style: Parameter 'os' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/blockwise_sa.h:573:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/blockwise_sa.h:632:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/blockwise_sa.h:973:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/blockwise_sa.h:1040:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.h:1289:27: style: Parameter 'quals' can be declared as pointer to const [constParameterPointer]
bowtie-1.3.1/ebwt.h:1290:27: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
bowtie-1.3.1/ebwt.h:1606:4: style: Variable 'u32ebwt' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/ebwt.h:1615:4: style: Variable 'u32ebwt' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/reference.h:63:14: style: Variable 'f4' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/reference.h:491:12: style: Variable 'dest_2' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/timer.h:134:13: style: Variable 'current' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/bitset.h:20:43: style: Parameter 'words' can be declared as pointer to const [constParameterPointer]
bowtie-1.3.1/ebwt_search_backtrack.h:1286:40: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
bowtie-1.3.1/ebwt_search_backtrack.h:1291:40: style: Parameter 'pairs' can be declared as pointer to const [constParameterPointer]
bowtie-1.3.1/ebwt_search_backtrack.h:1669:40: style: Parameter 'elims' can be declared as pointer to const [constParameterPointer]
bowtie-1.3.1/range_source.h:1241:11: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/range_source.h:1263:12: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/range_source.h:1348:12: style: Variable 'newtop' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/range_source.h:1444:4: style: Variable 'popped' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/range_source.h:1478:5: style: Variable 'popped' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/range_source.h:1507:5: style: Variable 'popped' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/sequence_io.h:167:11: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
bowtie-1.3.1/bitpack.h:26:18: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 25. [shiftTooManyBits]
bowtie-1.3.1/bitpack.h:25:2: note: Assuming that condition 'off<16' is not redundant
bowtie-1.3.1/bitpack.h:26:18: note: Shift
bowtie-1.3.1/bitpack.h:31:19: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 30. [shiftTooManyBits]
bowtie-1.3.1/bitpack.h:30:2: note: Assuming that condition 'off<16' is not redundant
bowtie-1.3.1/bitpack.h:31:19: note: Shift
bowtie-1.3.1/reference.h:505:18: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/ebwt_search_backtrack.h:1673:38: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/ebwt_search_backtrack.h:2729:42: style: Variable 'sLeft' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/ebwt.h:3894:11: style: Unused variable: name [unusedVariable]
bowtie-1.3.1/bowtie_inspect.cpp:287:18: style: Variable 'tlen' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/range_source.h:1245:44: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bowtie-1.3.1/range_source.h:1262:44: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bowtie-1.3.1/bowtie_main.cpp:51:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bowtie_main.cpp:44:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
bowtie-1.3.1/bowtie_main.cpp:42:46: note: Assuming allocation function fails
bowtie-1.3.1/bowtie_main.cpp:42:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
bowtie-1.3.1/bowtie_main.cpp:44:5: note: Null pointer dereference
bowtie-1.3.1/bowtie_main.cpp:42:27: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/bt2_locks.cpp:8:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bt2_locks.cpp:18:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bt2_locks.cpp:32:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/bt2_locks.cpp:37:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:690:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:701:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/chaincat.cpp:20:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sstring.h:586:14: warning: Member variable 'SString::cs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
bowtie-1.3.1/sstring.h:586:14: warning: Member variable 'SString::printcs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
bowtie-1.3.1/sstring.h:586:14: warning: Member variable 'SString::len_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
bowtie-1.3.1/sstring.h:735:7: style:inconclusive: Technically the member function 'SString::operator==' can be const. [functionConst]
bowtie-1.3.1/sstring.h:742:7: style:inconclusive: Technically the member function 'SString::operator!=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:749:7: style:inconclusive: Technically the member function 'SString::operator<' can be const. [functionConst]
bowtie-1.3.1/sstring.h:756:7: style:inconclusive: Technically the member function 'SString::operator>' can be const. [functionConst]
bowtie-1.3.1/sstring.h:763:7: style:inconclusive: Technically the member function 'SString::operator<=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:770:7: style:inconclusive: Technically the member function 'SString::operator>=' can be const. [functionConst]
bowtie-1.3.1/sstring.h:687:15: style: Virtual function 'install' is called from constructor 'SString(const std::basic_string<T>&str)' at line 543. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:543:3: note: Calling install
bowtie-1.3.1/sstring.h:687:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:687:15: style: Virtual function 'install' is called from constructor 'SString(const T*b,long sz)' at line 554. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:554:3: note: Calling install
bowtie-1.3.1/sstring.h:687:15: note: install is a virtual function
bowtie-1.3.1/sstring.h:687:15: style: Virtual function 'install' is called from constructor 'SString(const T*b)' at line 565. Dynamic binding is not used. [virtualCallInConstructor]
bowtie-1.3.1/sstring.h:565:3: note: Calling install
bowtie-1.3.1/sstring.h:687:15: note: install is a virtual function
bowtie-1.3.1/chaincat.cpp:34:26: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt.cpp:42:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_build.cpp:110:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_build.cpp:218:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_build.cpp:311:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_build.cpp:191:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_build.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie-1.3.1/ebwt_build.cpp:534:13: style: Condition 'optind>=argc' is always false [knownConditionTrueFalse]
bowtie-1.3.1/ebwt_build.cpp:526:13: note: Assuming that condition 'optind>=argc' is not redundant
bowtie-1.3.1/ebwt_build.cpp:534:13: note: Condition 'optind>=argc' is always false
bowtie-1.3.1/ebwt_build.cpp:601:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt_build.cpp:620:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie-1.3.1/ebwt_build.cpp:203:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bowtie-1.3.1/ebwt_search_backtrack.h:242:7: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:242:7: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:917:10: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:917:10: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:1310:7: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:1310:7: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:1350:7: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:1350:7: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:1927:7: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:1927:7: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:2492:7: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:2492:7: note: Shadow variable
bowtie-1.3.1/ebwt_search_backtrack.h:2532:7: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt_search_backtrack.h:2532:7: note: Shadow variable
bowtie-1.3.1/ebwt.h:2716:17: style: Local variable 'offRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:40:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2716:17: note: Shadow variable
bowtie-1.3.1/ebwt.h:2951:11: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:38:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2951:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:2953:11: style: Local variable 'linesPerSide' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:39:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2953:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:2955:11: style: Local variable 'offRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:40:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2955:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:2961:11: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2961:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:3469:11: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:38:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3469:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:3470:11: style: Local variable 'linesPerSide' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:39:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3470:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:3471:11: style: Local variable 'offRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:40:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3471:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:3472:11: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_build.cpp:41:16: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3472:11: note: Shadow variable
bowtie-1.3.1/ebwt_build.cpp:596:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt_build.cpp:615:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt_build.cpp:629:26: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/range_cache.h:46:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:66:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:97:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:154:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:199:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:253:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:284:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:301:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:396:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_cache.h:421:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_chaser.h:54:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_chaser.h:132:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/range_chaser.h:184:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:76:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:141:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:195:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:280:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:526:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:621:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:927:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:1037:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:1402:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:1524:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:1974:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:2151:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:2574:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:2773:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:3310:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:3527:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:4167:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_aligner.h:4404:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner_seed_mm.h:527:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner_seed_mm.h:1315:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:443:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:553:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:569:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:583:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:617:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:1347:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/search_1mm_phase1.c:13:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:1721:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/search_23mm_phase1.c:14:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:2209:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/search_seeded_phase1.c:13:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:2750:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:2947:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:2963:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:1578:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:1622:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:1877:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:745:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:818:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:957:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:1111:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:442:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/aligner.h:514:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ebwt_search.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie-1.3.1/aligner.h:508:45: warning: Assert statement calls a function which may have desired side effects: 'range'. [assertWithSideEffect]
bowtie-1.3.1/ebwt_search.cpp:1074:17: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
bowtie-1.3.1/range_cache.h:131:2: warning: Member variable 'RangeCacheEntry::verbose_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/range_cache.h:139:2: warning: Member variable 'RangeCacheEntry::verbose_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ref_aligner.h:39:2: warning: Member variable 'RefAligner::buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/aligner.h:47:2: warning: Member variable 'Aligner::alen_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/aligner.h:47:2: warning: Member variable 'Aligner::blen_' is not initialized in the constructor. [uninitMemberVar]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < Range , 128 >::cat_' is not assigned a value in 'EList < Range , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < Aligner * , 128 >::cat_' is not assigned a value in 'EList < Aligner * , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < RangeSourceDriver < EbwtRangeSource > * , 128 >::cat_' is not assigned a value in 'EList < RangeSourceDriver < EbwtRangeSource > * , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < std :: thread * , 128 >::cat_' is not assigned a value in 'EList < std :: thread * , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/ds.h:394:15: warning: Member variable 'EList < thread_tracking_pair , 128 >::cat_' is not assigned a value in 'EList < thread_tracking_pair , 128 >::operator='. [operatorEqVarError]
bowtie-1.3.1/aligner.h:572:26: style:inconclusive: Member variable 'UnpairedAlignerV2 < EbwtRangeSource >::refs_' is in the wrong place in the initializer list. [initializerList]
bowtie-1.3.1/aligner.h:406:3: note: Member variable 'UnpairedAlignerV2 < EbwtRangeSource >::refs_' is in the wrong place in the initializer list.
bowtie-1.3.1/aligner.h:572:26: note: Member variable 'UnpairedAlignerV2 < EbwtRangeSource >::refs_' is in the wrong place in the initializer list.
bowtie-1.3.1/range_cache.h:109:14: style:inconclusive: Technically the member function 'RangeCacheMemPool::closed' can be const. [functionConst]
bowtie-1.3.1/range_chaser.h:215:7: performance:inconclusive: Technically the member function 'RangeChaser::prep' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Range , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Range , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Aligner * , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Aligner * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < RangeSourceDriver < EbwtRangeSource > * , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < RangeSourceDriver < EbwtRangeSource > * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: thread * , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: thread * , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/ds.h:532:7: style:inconclusive: Technically the member function 'EList < thread_tracking_pair , 128 >::fillZero' can be const. [functionConst]
bowtie-1.3.1/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < thread_tracking_pair , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/range_cache.h:43:5: warning: Class 'RangeCacheMemPool' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/range_cache.h:43:5: warning: Class 'RangeCacheMemPool' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/aligner.h:223:3: warning: Class 'MixedMultiAligner' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie-1.3.1/aligner.h:223:3: warning: Class 'MixedMultiAligner' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie-1.3.1/aligner.h:1330:26: warning: The class 'PairedBWAlignerV1 < EbwtRangeSource >' defines member variable with name 'patsrc_' also defined in its parent class 'Aligner'. [duplInheritedMember]
bowtie-1.3.1/aligner.h:77:26: note: Parent variable 'Aligner::patsrc_'
bowtie-1.3.1/aligner.h:1330:26: note: Derived variable 'PairedBWAlignerV1 < EbwtRangeSource >::patsrc_'
bowtie-1.3.1/aligner.h:2001:26: warning: The class 'PairedBWAlignerV2 < EbwtRangeSource >' defines member variable with name 'patsrc_' also defined in its parent class 'Aligner'. [duplInheritedMember]
bowtie-1.3.1/aligner.h:77:26: note: Parent variable 'Aligner::patsrc_'
bowtie-1.3.1/aligner.h:2001:26: note: Derived variable 'PairedBWAlignerV2 < EbwtRangeSource >::patsrc_'
bowtie-1.3.1/range_cache.h:37:2: style: Class 'RangeCacheMemPool' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/range_cache.h:131:2: style: Class 'RangeCacheEntry' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie-1.3.1/ref_aligner.h:175:11: style: The destructor '~ExactRefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:175:11: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:267:15: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:267:15: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:506:11: style: The destructor '~OneMMRefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:506:11: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:608:17: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:608:17: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:907:12: style: The destructor '~TwoMMRefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:907:12: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:1024:18: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:1024:18: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:1382:13: style: The destructor '~ThreeMMRefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:1382:13: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:1511:19: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:1511:19: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:1932:14: style: The destructor '~Seed0RefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:1932:14: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:2138:20: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:2138:20: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:2532:15: style: The destructor '~Seed1RefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:2532:15: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:2760:21: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:2760:21: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:3268:16: style: The destructor '~Seed2RefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:3268:16: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:3514:22: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:3514:22: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:4125:17: style: The destructor '~Seed3RefAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:53:11: note: Virtual destructor in base class
bowtie-1.3.1/ref_aligner.h:4125:17: note: Destructor in derived class
bowtie-1.3.1/ref_aligner.h:4391:23: style: The function 'anchor64Find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/ref_aligner.h:105:15: note: Virtual function in base class
bowtie-1.3.1/ref_aligner.h:4391:23: note: Function in derived class
bowtie-1.3.1/aligner_0mm.h:69:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_0mm.h:69:19: note: Function in derived class
bowtie-1.3.1/aligner_0mm.h:206:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_0mm.h:206:19: note: Function in derived class
bowtie-1.3.1/aligner_1mm.h:73:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_1mm.h:73:19: note: Function in derived class
bowtie-1.3.1/aligner_1mm.h:249:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_1mm.h:249:19: note: Function in derived class
bowtie-1.3.1/aligner_23mm.h:74:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_23mm.h:74:19: note: Function in derived class
bowtie-1.3.1/aligner_23mm.h:322:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_23mm.h:322:19: note: Function in derived class
bowtie-1.3.1/aligner_seed_mm.h:80:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_seed_mm.h:80:19: note: Function in derived class
bowtie-1.3.1/aligner_seed_mm.h:650:19: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:92:19: note: Virtual function in base class
bowtie-1.3.1/aligner_seed_mm.h:650:19: note: Function in derived class
bowtie-1.3.1/sam.h:72:15: style: The function 'append' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:206:15: note: Virtual function in base class
bowtie-1.3.1/sam.h:72:15: note: Function in derived class
bowtie-1.3.1/sam.h:102:15: style: The function 'reportMaxed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:494:15: note: Virtual function in base class
bowtie-1.3.1/sam.h:102:15: note: Function in derived class
bowtie-1.3.1/sam.h:110:15: style: The function 'reportUnaligned' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/hit.h:506:15: note: Virtual function in base class
bowtie-1.3.1/sam.h:110:15: note: Function in derived class
bowtie-1.3.1/aligner.h:1550:11: style: The destructor '~PairedBWAlignerV2 < EbwtRangeSource >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:52:11: note: Virtual destructor in base class
bowtie-1.3.1/aligner.h:1550:11: note: Destructor in derived class
bowtie-1.3.1/aligner.h:1570:15: style: The function 'setQuery' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:57:15: note: Virtual function in base class
bowtie-1.3.1/aligner.h:1570:15: note: Function in derived class
bowtie-1.3.1/aligner.h:1608:15: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:54:15: note: Virtual function in base class
bowtie-1.3.1/aligner.h:1608:15: note: Function in derived class
bowtie-1.3.1/aligner.h:722:11: style: The destructor '~PairedBWAlignerV1 < EbwtRangeSource >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:52:11: note: Virtual destructor in base class
bowtie-1.3.1/aligner.h:722:11: note: Destructor in derived class
bowtie-1.3.1/aligner.h:737:15: style: The function 'setQuery' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:57:15: note: Virtual function in base class
bowtie-1.3.1/aligner.h:737:15: note: Function in derived class
bowtie-1.3.1/aligner.h:815:15: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:54:15: note: Virtual function in base class
bowtie-1.3.1/aligner.h:815:15: note: Function in derived class
bowtie-1.3.1/aligner.h:423:11: style: The destructor '~UnpairedAlignerV2 < EbwtRangeSource >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:52:11: note: Virtual destructor in base class
bowtie-1.3.1/aligner.h:423:11: note: Destructor in derived class
bowtie-1.3.1/aligner.h:434:15: style: The function 'setQuery' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:57:15: note: Virtual function in base class
bowtie-1.3.1/aligner.h:434:15: note: Function in derived class
bowtie-1.3.1/aligner.h:503:15: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/aligner.h:54:15: note: Virtual function in base class
bowtie-1.3.1/aligner.h:503:15: note: Function in derived class
bowtie-1.3.1/range_source.h:1904:11: style: The destructor '~StubRangeSourceDriver < EbwtRangeSource >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1622:11: note: Virtual destructor in base class
bowtie-1.3.1/range_source.h:1904:11: note: Destructor in derived class
bowtie-1.3.1/range_source.h:1907:15: style: The function 'setQueryImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1636:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1907:15: note: Function in derived class
bowtie-1.3.1/range_source.h:1910:15: style: The function 'advanceImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1662:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1910:15: note: Function in derived class
bowtie-1.3.1/range_source.h:1913:17: style: The function 'range' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1666:17: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1913:17: note: Function in derived class
bowtie-1.3.1/range_source.h:1919:15: style: The function 'mate1' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1672:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1919:15: note: Function in derived class
bowtie-1.3.1/range_source.h:1926:15: style: The function 'fw' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie-1.3.1/range_source.h:1677:15: note: Virtual function in base class
bowtie-1.3.1/range_source.h:1926:15: note: Function in derived class
bowtie-1.3.1/ref_aligner.h:1711:18: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
bowtie-1.3.1/ref_aligner.h:1706:24: note: outer condition: nPoss>1
bowtie-1.3.1/ref_aligner.h:1711:18: note: identical inner condition: nPoss>1
bowtie-1.3.1/ref_aligner.h:4660:22: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
bowtie-1.3.1/ref_aligner.h:4646:28: note: outer condition: nPoss>1
bowtie-1.3.1/ref_aligner.h:4660:22: note: identical inner condition: nPoss>1
bowtie-1.3.1/range_cache.h:327:42: style: Return value 'RangeCacheEntry::sanityCheckEnts(len_,ents_,ebwt_)' is always true [knownConditionTrueFalse]
bowtie-1.3.1/range_cache.h:327:42: note: Calling function 'sanityCheckEnts' returns 1
bowtie-1.3.1/range_cache.h:327:42: note: Return value 'RangeCacheEntry::sanityCheckEnts(len_,ents_,ebwt_)' is always true
bowtie-1.3.1/ref_aligner.h:1216:17: style: Condition 'nPoss==2' is always true [knownConditionTrueFalse]
bowtie-1.3.1/ref_aligner.h:1211:23: note: Assuming that condition 'nPoss>1' is not redundant
bowtie-1.3.1/ref_aligner.h:1208:16: note: Assuming that condition 'diffs>2' is not redundant
bowtie-1.3.1/ref_aligner.h:1211:36: note: Assuming that condition 'diffs==nPoss' is not redundant
bowtie-1.3.1/ref_aligner.h:1216:17: note: Condition 'nPoss==2' is always true
bowtie-1.3.1/aligner.h:64:18: style: Condition 'bufb_!=NULL' is always true [knownConditionTrueFalse]
bowtie-1.3.1/aligner_23mm.h:403:44: style: Condition 'two_' is always false [knownConditionTrueFalse]
bowtie-1.3.1/aligner_23mm.h:401:7: note: Assuming that condition '!two_' is not redundant
bowtie-1.3.1/aligner_23mm.h:403:44: note: Condition 'two_' is always false
bowtie-1.3.1/aligner_23mm.h:468:44: style: Condition 'two_' is always false [knownConditionTrueFalse]
bowtie-1.3.1/aligner_23mm.h:466:7: note: Assuming that condition '!two_' is not redundant
bowtie-1.3.1/aligner_23mm.h:468:44: note: Condition 'two_' is always false
bowtie-1.3.1/aligner_23mm.h:532:44: style: Condition 'two_' is always false [knownConditionTrueFalse]
bowtie-1.3.1/aligner_23mm.h:531:7: note: Assuming that condition '!two_' is not redundant
bowtie-1.3.1/aligner_23mm.h:532:44: note: Condition 'two_' is always false
bowtie-1.3.1/aligner_23mm.h:596:44: style: Condition 'two_' is always false [knownConditionTrueFalse]
bowtie-1.3.1/aligner_23mm.h:595:7: note: Assuming that condition '!two_' is not redundant
bowtie-1.3.1/aligner_23mm.h:596:44: note: Condition 'two_' is always false
bowtie-1.3.1/aligner_seed_mm.h:326:22: style: Condition 'seedMms_>2' is always true [knownConditionTrueFalse]
bowtie-1.3.1/aligner_seed_mm.h:213:22: note: Assuming that condition 'seedMms_==2' is not redundant
bowtie-1.3.1/aligner_seed_mm.h:326:22: note: Condition 'seedMms_>2' is always true
bowtie-1.3.1/aligner_seed_mm.h:953:22: style: Condition 'seedMms_>1' is always true [knownConditionTrueFalse]
bowtie-1.3.1/aligner_seed_mm.h:775:22: note: Assuming that condition 'seedMms_==1' is not redundant
bowtie-1.3.1/aligner_seed_mm.h:953:22: note: Condition 'seedMms_>1' is always true
bowtie-1.3.1/ebwt_search.cpp:1062:18: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: fname [nullPointerOutOfMemory]
bowtie-1.3.1/ebwt_search.cpp:1060:30: note: Assuming allocation function fails
bowtie-1.3.1/ebwt_search.cpp:1060:16: note: Assignment 'fname=(char*)std::calloc(FNAME_SIZE,sizeof(char))', assigned value is 0
bowtie-1.3.1/ebwt_search.cpp:1062:18: note: Null pointer dereference
bowtie-1.3.1/ebwt_search.cpp:1063:9: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
bowtie-1.3.1/ebwt_search.cpp:1062:17: note: Assuming allocation function fails
bowtie-1.3.1/ebwt_search.cpp:1062:17: note: Assignment 'f=std::fopen(fname,"w")', assigned value is 0
bowtie-1.3.1/ebwt_search.cpp:1063:9: note: Null pointer dereference
bowtie-1.3.1/ref_aligner.h:86:20: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1044:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1060:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1071:16: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1131:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1224:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1392:32: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1394:24: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1399:67: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1401:59: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1438:68: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1440:60: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1510:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1607:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1773:39: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1775:31: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1780:74: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1782:66: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1819:75: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1821:67: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:1956:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2057:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2269:45: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2271:41: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2276:80: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2278:76: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2315:81: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2317:77: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2379:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2610:28: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2815:41: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2817:33: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2822:76: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2824:68: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2861:77: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:2863:69: style: C-style pointer casting [cstyleCast]
bowtie-1.3.1/ebwt_search.cpp:562:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bowtie-1.3.1/range_cache.h:395:15: style: The scope of the variable 'jumps' can be reduced. [variableScope]
bowtie-1.3.1/range_cache.h:426:28: style: The scope of the variable 'newbot' can be reduced. [variableScope]
bowtie-1.3.1/ref_aligner.h:2334:22: style: The scope of the variable 'ham' can be reduced. [variableScope]
bowtie-1.3.1/aligner.h:259:8: style: The scope of the variable 'saw_last_read' can be reduced. [variableScope]
bowtie-1.3.1/ebwt_search.cpp:1070:17: style: The scope of the variable 'ent' can be reduced. [variableScope]
bowtie-1.3.1/ebwt_search.cpp:1677:13: style: The scope of the variable 's3' can be reduced. [variableScope]
bowtie-1.3.1/ebwt_search.cpp:3322:10: style: The scope of the variable 'query' can be reduced. [variableScope]
bowtie-1.3.1/ebwt_search.cpp:3324:10: style: The scope of the variable 'outfile' can be reduced. [variableScope]
bowtie-1.3.1/ref_aligner.h:802:7: style: Unsigned expression 'mmpos' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:1234:8: style: Unsigned expression 'mmpos1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:1254:9: style: Unsigned expression 'mmpos2' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:1733:9: style: Unsigned expression 'mmpos1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:1753:10: style: Unsigned expression 'mmpos2' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:1782:11: style: Unsigned expression 'mmpos3' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:3018:11: style: Unsigned expression 'mmpos' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:3803:12: style: Unsigned expression 'mmpos1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:3834:13: style: Unsigned expression 'mmpos2' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:4700:13: style: Unsigned expression 'mmpos1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:4732:14: style: Unsigned expression 'mmpos2' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_aligner.h:4772:15: style: Unsigned expression 'mmpos3' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ebwt.h:2716:17: style: Local variable 'offRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:73:12: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2716:17: note: Shadow variable
bowtie-1.3.1/ebwt.h:2955:11: style: Local variable 'offRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:73:12: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2955:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:2960:11: style: Local variable 'isaRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:74:12: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:2960:11: note: Shadow variable
bowtie-1.3.1/ebwt.h:3471:11: style: Local variable 'offRate' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:73:12: note: Shadowed declaration
bowtie-1.3.1/ebwt.h:3471:11: note: Shadow variable
bowtie-1.3.1/range_cache.h:503:15: style: Local variable 'jumps' shadows outer variable [shadowVariable]
bowtie-1.3.1/range_cache.h:427:14: note: Shadowed declaration
bowtie-1.3.1/range_cache.h:503:15: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:2471:21: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:2282:19: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:2471:21: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:2476:21: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:2282:19: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:2476:21: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:2493:21: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:2282:19: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:2493:21: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:2620:13: style: Local variable 'seedMms' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:81:12: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:2620:13: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:3183:22: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:2919:22: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:3183:22: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:3188:22: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:2919:22: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:3188:22: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:3218:22: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:2919:22: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:3218:22: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:3356:14: style: Local variable 'seedMms' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:81:12: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:3356:14: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:4016:23: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:3684:21: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:4016:23: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:4021:23: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:3684:21: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:4021:23: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:4063:23: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:3684:21: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:4063:23: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:4215:15: style: Local variable 'seedMms' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:81:12: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:4215:15: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:4971:24: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:4565:22: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:4971:24: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:4976:24: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:4565:22: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:4976:24: note: Shadow variable
bowtie-1.3.1/ref_aligner.h:5029:24: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/ref_aligner.h:4565:22: note: Shadowed declaration
bowtie-1.3.1/ref_aligner.h:5029:24: note: Shadow variable
bowtie-1.3.1/aligner.h:319:10: style: Local variable 'saw_last_read' shadows outer variable [shadowVariable]
bowtie-1.3.1/aligner.h:259:8: note: Shadowed declaration
bowtie-1.3.1/aligner.h:319:10: note: Shadow variable
bowtie-1.3.1/ebwt_search.cpp:3222:19: style: Local variable 'refnames' shadows outer variable [shadowVariable]
bowtie-1.3.1/ebwt_search.cpp:3194:18: note: Shadowed declaration
bowtie-1.3.1/ebwt_search.cpp:3222:19: note: Shadow variable
bowtie-1.3.1/range_cache.h:45:28: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ref_aligner.h:140:27: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/ebwt_search.cpp:3449:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie-1.3.1/aligner.h:1500:12: style: Parameter 'sink' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/aligner.h:388:12: style: Parameter 'sink' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/aligner.h:391:24: style: Parameter 'os' can be declared as reference to const [constParameterReference]
bowtie-1.3.1/ebwt_search.cpp:1070:17: style: Variable 'ent' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/range_cache.h:454:18: style: Variable 'ents' can be declared as pointer to const [constVariablePointer]
bowtie-1.3.1/range_cache.h:395:21: style: Variable 'jumps' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/range_cache.h:426:21: style: Variable 'newtop' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/range_cache.h:426:35: style: Variable 'newbot' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/ebwt_search.cpp:1433:23: style: Variable 'tids[nthreads-1]' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/ebwt_search.cpp:1814:23: style: Variable 'tids[nthreads-1]' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/ebwt_search.cpp:2310:23: style: Variable 'tids[nthreads-1]' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/ebwt_search.cpp:2856:23: style: Variable 'tids[nthreads-1]' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/aligner.h:1594:33: style: Variable 'doneSe2_' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/range_cache.h:392:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bowtie-1.3.1/ebwt_search_util.cpp:20:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.cpp:25:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.cpp:117:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit.h:242:44: warning: Possible null pointer dereference: hsptr [nullPointer]
bowtie-1.3.1/hit.cpp:65:19: note: Calling function 'reportHits', 2nd argument 'NULL' value is 0
bowtie-1.3.1/hit.h:242:44: note: Null pointer dereference
bowtie-1.3.1/hit.h:247:38: warning: Possible null pointer dereference: hsptr [nullPointer]
bowtie-1.3.1/hit.cpp:65:19: note: Calling function 'reportHits', 2nd argument 'NULL' value is 0
bowtie-1.3.1/hit.h:247:38: note: Null pointer dereference
bowtie-1.3.1/hit.cpp:41:32: error: Division by zero. [zerodiv]
bowtie-1.3.1/hit.cpp:29:10: note: Assignment 'num=0', assigned value is 0
bowtie-1.3.1/hit.cpp:31:24: note: Assuming condition is false
bowtie-1.3.1/hit.cpp:41:32: note: Division by zero
bowtie-1.3.1/hit.cpp:294:31: style: Variable 'firstfield' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/hit_set.cpp:30:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.cpp:59:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/hit_set.cpp:42:14: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/hit_set.cpp:24:10: note: Shadowed declaration
bowtie-1.3.1/hit_set.cpp:42:14: note: Shadow variable
bowtie-1.3.1/pat.cpp:35:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:105:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:155:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:195:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:255:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:285:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:376:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:461:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:540:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:605:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:757:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:810:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:875:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:1042:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:1186:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:1216:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:1223:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:1229:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:1235:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/pat.cpp:64:30: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalize' can be const. [functionConst]
bowtie-1.3.1/pat.h:1017:7: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
bowtie-1.3.1/pat.cpp:64:30: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
bowtie-1.3.1/pat.cpp:76:30: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalizePair' can be const. [functionConst]
bowtie-1.3.1/pat.h:1024:7: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
bowtie-1.3.1/pat.cpp:76:30: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
bowtie-1.3.1/pat.cpp:465:18: style: Condition 'endi>0' is always true [knownConditionTrueFalse]
bowtie-1.3.1/pat.cpp:454:11: note: Assuming that condition 'endi<1' is not redundant
bowtie-1.3.1/pat.cpp:465:18: note: Condition 'endi>0' is always true
bowtie-1.3.1/pat.cpp:1046:18: style: Condition 'endi>0' is always true [knownConditionTrueFalse]
bowtie-1.3.1/pat.cpp:1035:11: note: Assuming that condition 'endi<1' is not redundant
bowtie-1.3.1/pat.cpp:1046:18: note: Condition 'endi>0' is always true
bowtie-1.3.1/pat.cpp:752:4: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie-1.3.1/pat.cpp:747:8: note: c is initialized
bowtie-1.3.1/pat.cpp:752:4: note: c is overwritten
bowtie-1.3.1/pat.cpp:255:2: style: Unsigned expression 'nread' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/pat.cpp:360:23: style:inconclusive: Function 'VectorPatternSource' argument 1 names different: declaration 'v' definition 'seqs'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:263:24: note: Function 'VectorPatternSource' argument 1 names different: declaration 'v' definition 'seqs'.
bowtie-1.3.1/pat.cpp:360:23: note: Function 'VectorPatternSource' argument 1 names different: declaration 'v' definition 'seqs'.
bowtie-1.3.1/pat.cpp:534:9: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:497:10: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:534:9: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:575:38: style:inconclusive: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:487:27: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie-1.3.1/pat.cpp:575:38: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie-1.3.1/pat.cpp:654:9: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:636:10: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:654:9: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:800:9: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:716:10: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:800:9: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:862:38: style:inconclusive: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:702:27: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie-1.3.1/pat.cpp:862:38: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie-1.3.1/pat.cpp:983:9: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:568:10: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:983:9: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:1132:9: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:777:10: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:1132:9: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie-1.3.1/pat.cpp:1168:36: style:inconclusive: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'. [funcArgNamesDifferent]
bowtie-1.3.1/pat.h:767:27: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie-1.3.1/pat.cpp:1168:36: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie-1.3.1/pat.cpp:393:15: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie-1.3.1/pat.cpp:373:13: note: Shadowed declaration
bowtie-1.3.1/pat.cpp:393:15: note: Shadow variable
bowtie-1.3.1/pat.cpp:832:15: style: Variable 'newlines' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/pat.cpp:1177:8: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
bowtie-1.3.1/random_test.cpp:20:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/endian_swap.h:109:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/word_io.h:39:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/word_io.h:73:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/word_io.h:110:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_read.cpp:31:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_read.cpp:146:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_read.cpp:163:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_read.cpp:215:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/ref_read.cpp:265:2: style: Unsigned expression 'bothTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/ref_read.cpp:266:2: style: Unsigned expression 'unambigTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie-1.3.1/sam.cpp:48:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BOWTIE_VERSION [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sam.cpp:119:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable flushed [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sam.cpp:181:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sam.cpp:272:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie-1.3.1/sam.cpp:20:18: performance:inconclusive: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie-1.3.1/sam.h:77:7: note: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace).
bowtie-1.3.1/sam.cpp:20:18: note: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace).
bowtie-1.3.1/sam.cpp:106:30: style: Condition 'paired' is always true [knownConditionTrueFalse]
bowtie-1.3.1/sam.cpp:99:5: note: Assuming that condition 'paired' is not redundant
bowtie-1.3.1/sam.cpp:102:22: note: Assuming condition is false
bowtie-1.3.1/sam.cpp:106:30: note: Condition 'paired' is always true
bowtie-1.3.1/hit.h:242:44: warning: Possible null pointer dereference: hsptr [nullPointer]
bowtie-1.3.1/sam.cpp:309:23: note: Calling function 'reportHits', 2nd argument 'NULL' value is 0
bowtie-1.3.1/hit.h:242:44: note: Null pointer dereference
bowtie-1.3.1/hit.h:247:38: warning: Possible null pointer dereference: hsptr [nullPointer]
bowtie-1.3.1/sam.cpp:309:23: note: Calling function 'reportHits', 2nd argument 'NULL' value is 0
bowtie-1.3.1/hit.h:247:38: note: Null pointer dereference
bowtie-1.3.1/sam.cpp:288:32: error: Division by zero. [zerodiv]
bowtie-1.3.1/sam.cpp:276:10: note: Assignment 'num=0', assigned value is 0
bowtie-1.3.1/sam.cpp:278:24: note: Assuming condition is false
bowtie-1.3.1/sam.cpp:288:32: note: Division by zero
bowtie-1.3.1/search_seeded_phase2.c:73:25: error: syntax error [syntaxError]
diff:
head bowtie-1.3.1/bowtie_build_main.cpp:44:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
     bowtie-1.3.1/bowtie_build_main.cpp:42:46: note: Assuming allocation function fails
     bowtie-1.3.1/bowtie_build_main.cpp:42:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
     bowtie-1.3.1/bowtie_build_main.cpp:44:5: note: Null pointer dereference
head bowtie-1.3.1/bowtie_main.cpp:44:5: warning: If memory allocation fails, then there is a possible null pointer dereference: myargs [nullPointerOutOfMemory]
     bowtie-1.3.1/bowtie_main.cpp:42:46: note: Assuming allocation function fails
     bowtie-1.3.1/bowtie_main.cpp:42:26: note: Assignment 'myargs=(const char**)std::malloc(sizeof(char*)*args.size())', assigned value is 0
     bowtie-1.3.1/bowtie_main.cpp:44:5: note: Null pointer dereference
head bowtie-1.3.1/ds.h:687:3: debug: CheckClass::isMemberVar found used member variable 'cur_' with varid 0 [varid0]
head bowtie-1.3.1/ds.h:687:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur_ [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/ds.h:758:3: debug: CheckClass::isMemberVar found used member variable 'cur_' with varid 0 [varid0]
head bowtie-1.3.1/ds.h:758:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur_ [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/ds.h:759:10: debug: CheckClass::isMemberVar found used member variable 'list_' with varid 0 [varid0]
head bowtie-1.3.1/ds.h:857:32: debug: CheckClass::isMemberVar found used member variable 'list_' with varid 0 [varid0]
head bowtie-1.3.1/ds.h:857:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable list_ [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/ds.h:879:15: debug: CheckClass::isMemberVar found used member variable 'cur_' with varid 0 [varid0]
head bowtie-1.3.1/ds.h:879:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cur_ [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/ds.h:887:7: debug: CheckClass::isMemberVar found used member variable 'list_' with varid 0 [varid0]
head bowtie-1.3.1/ebwt_search.cpp:1062:18: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: fname [nullPointerOutOfMemory]
     bowtie-1.3.1/ebwt_search.cpp:1060:30: note: Assuming allocation function fails
     bowtie-1.3.1/ebwt_search.cpp:1060:16: note: Assignment 'fname=(char*)std::calloc(FNAME_SIZE,sizeof(char))', assigned value is 0
     bowtie-1.3.1/ebwt_search.cpp:1062:18: note: Null pointer dereference
head bowtie-1.3.1/ebwt_search.cpp:1063:9: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
     bowtie-1.3.1/ebwt_search.cpp:1062:17: note: Assuming allocation function fails
     bowtie-1.3.1/ebwt_search.cpp:1062:17: note: Assignment 'f=std::fopen(fname,"w")', assigned value is 0
     bowtie-1.3.1/ebwt_search.cpp:1063:9: note: Null pointer dereference
head bowtie-1.3.1/ebwt_search_backtrack.h:2192:65: style: C-style pointer casting [cstyleCast]
2.17.0 bowtie-1.3.1/hit.h:199:3: error: Exception thrown in function declared not to throw exceptions. [throwInNoexceptFunction]
head bowtie-1.3.1/pat.cpp:64:30: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalize' can be const. [functionConst]
     bowtie-1.3.1/pat.h:1017:7: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
     bowtie-1.3.1/pat.cpp:64:30: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
head bowtie-1.3.1/pat.cpp:76:30: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalizePair' can be const. [functionConst]
     bowtie-1.3.1/pat.h:1024:7: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
     bowtie-1.3.1/pat.cpp:76:30: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
2.17.0 bowtie-1.3.1/pat.h:1017:7: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalize' can be const. [functionConst]
     bowtie-1.3.1/pat.cpp:64:30: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
     bowtie-1.3.1/pat.h:1017:7: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
2.17.0 bowtie-1.3.1/pat.h:1024:7: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalizePair' can be const. [functionConst]
     bowtie-1.3.1/pat.cpp:76:30: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
     bowtie-1.3.1/pat.h:1024:7: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
head bowtie-1.3.1/sam.cpp:20:18: performance:inconclusive: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bowtie-1.3.1/sam.h:77:7: note: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace).
     bowtie-1.3.1/sam.cpp:20:18: note: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace).
2.17.0 bowtie-1.3.1/sam.h:77:7: performance:inconclusive: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bowtie-1.3.1/sam.cpp:20:18: note: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace).
     bowtie-1.3.1/sam.h:77:7: note: Technically the member function 'SAMHitSink::appendHeaders' can be static (but you may consider moving to unnamed namespace).
2.17.0 bowtie-1.3.1/sstring.h:121:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:121:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:155:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:231:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:231:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:279:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:303:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:303:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:329:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:329:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:350:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:374:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:374:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:400:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:400:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:421:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:445:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:445:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:471:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie-1.3.1/sstring.h:471:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.17.0 bowtie-1.3.1/sstring.h:96:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]


DONE