2025-01-27 02:32
ftp://ftp.de.debian.org/debian/pool/main/b/bowtie2/bowtie2_2.5.4.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-1016-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.59
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.16.0
head-info: 0eb54ba (2025-01-25 21:24:33 +0100)
count: 2521 2493
elapsed-time: 131.5 141.9
head-timing-info:

old-timing-info:

head results:
bowtie2-2.5.4/sstring.h:2824:37: debug: Failed to instantiate template "SStringExpandable". The checking continues anyway. [templateInstantiation]
bowtie2-2.5.4/assert_helpers.h:251:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/assert_helpers.h:269:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_locks.h:59:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_locks.h:65:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:85:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:122:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1050:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1059:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1079:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1094:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1119:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1179:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1187:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1195:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1259:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1289:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1330:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1353:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1394:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1403:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1423:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1438:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1461:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1519:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1527:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1535:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1548:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1556:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1599:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1629:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1670:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1693:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1739:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1751:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1764:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1786:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1793:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1897:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1924:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1972:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2015:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2032:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2079:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2088:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2108:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2123:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2148:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2237:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2245:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2293:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2323:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2361:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2384:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2432:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2515:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2534:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2558:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2575:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2598:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2627:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2646:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2688:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2705:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2938:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2946:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3137:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3411:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3431:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3440:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3449:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3458:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3482:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:4169:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/alphabet.h:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/alphabet.h:119:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:94:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:119:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:153:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:202:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:229:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:256:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:277:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:301:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:327:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:348:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:372:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:398:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:419:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:443:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:469:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:625:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:641:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:652:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:660:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:668:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:676:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:687:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:698:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:786:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:800:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:841:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1056:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1073:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1091:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1121:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1129:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1137:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1450:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1480:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1526:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1547:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2184:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2223:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2249:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2263:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2271:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2279:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2291:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2306:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2318:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2382:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2398:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2407:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2420:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2437:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2459:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2512:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2611:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2624:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2636:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2654:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2670:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2685:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2715:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2725:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2735:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2744:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2753:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2769:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2785:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2802:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3168:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3183:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3197:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3215:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3231:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3254:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3263:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3274:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3283:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3294:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3316:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3325:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3340:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3357:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3378:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:118:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:242:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:391:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:409:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:567:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:578:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:607:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:641:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:660:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:692:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:754:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:772:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:844:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:960:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/util.h:34:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_signed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/read.h:208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/read.h:220:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/read.h:229:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/read.h:241:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/read.h:318:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alignment [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/tokenize.h:45:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_cache.h:147:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_cache.h:375:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_cache.h:428:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_cache.h:955:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_cache.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_cache.cpp:46:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_cache.cpp:80:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2896:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2909:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2921:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2958:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2973:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2987:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3016:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3025:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3036:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3045:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3056:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3071:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3086:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3103:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1714:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1730:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1756:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1771:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1787:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1799:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1807:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1815:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1915:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1953:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1970:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2037:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2053:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3855:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3892:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3944:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3964:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3543:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3563:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3572:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3581:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3590:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3614:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3180:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3197:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3220:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3238:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3260:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3283:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3293:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3307:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3318:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3328:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3350:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:355:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:364:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:383:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:395:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:421:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:513:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:533:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:592:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:603:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:619:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:633:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:649:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:665:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:687:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:695:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:750:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:758:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:796:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:805:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:841:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:866:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:886:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:912:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:938:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:1001:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:4065:11: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie2-2.5.4/ds.h:4087:13: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie2-2.5.4/ds.h:4113:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie2-2.5.4/ds.h:4114:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie2-2.5.4/ds.h:4126:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie2-2.5.4/ds.h:4127:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie2-2.5.4/ds.h:4133:10: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
bowtie2-2.5.4/ref_coord.h:243:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ref_coord.h:408:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3176:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3193:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3216:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3234:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3260:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3269:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3305:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3316:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:3328:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:117:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:150:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:206:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:343:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:365:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:730:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:824:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1069:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1080:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1204:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1213:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1233:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/alphabet.h:92:16: warning: Either the condition '(c)<=4' is redundant or the array 'dnacomp[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie2-2.5.4/alphabet.h:91:2: note: Assuming that condition '(c)<=4' is not redundant
bowtie2-2.5.4/alphabet.h:92:16: note: Array index out of bounds
bowtie2-2.5.4/aligner_result.h:1243:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1252:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1262:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1282:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1314:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1350:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1521:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/qual.h:46:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/qual.h:108:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/qual.h:166:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/qual.h:197:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/qual.h:226:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:209:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:286:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:303:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:330:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:341:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:352:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/dp_framer.h:109:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:38:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:152:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:160:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:222:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:314:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:368:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:444:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:459:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sse_util.h:481:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:256:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:408:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:462:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:470:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:478:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:488:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:556:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_st_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:592:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.h:638:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/mask.h:57:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:122:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:134:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:146:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:158:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:170:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:182:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:223:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:441:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:466:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.h:491:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.cpp:54:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.cpp:604:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.cpp:1158:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.cpp:1247:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.cpp:1362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_bt.cpp:1475:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:114:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2364:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:2387:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/filebuf.h:445:18: 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]
bowtie2-2.5.4/filebuf.h:447:21: note: Assuming that condition 'c==-1' is not redundant
bowtie2-2.5.4/filebuf.h:445:18: note: Invalid argument
bowtie2-2.5.4/filebuf.h:484:18: 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]
bowtie2-2.5.4/filebuf.h:486:21: note: Assuming that condition 'c==-1' is not redundant
bowtie2-2.5.4/filebuf.h:484:18: note: Invalid argument
bowtie2-2.5.4/random_source.h:39:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/random_source.h:39:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/random_source.h:41:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/random_source.h:43:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/random_source.h:43:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/ds.h:1763:8: warning: Member variable 'ESet::cat_' is not assigned a value in 'ESet::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:2451:8: warning: Member variable 'EMap::cat_' is not assigned a value in 'EMap::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString::cs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString::printcs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString::len_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:2134:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:2146:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:2153:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:2160:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:2232:21: warning: Member variable 'SStringFixed::printcs_' is not assigned a value in 'SStringFixed::operator='. [operatorEqVarError]
bowtie2-2.5.4/filebuf.h:67:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:67:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:71:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:71:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:77:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:77:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:90:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:90:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:96:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:96:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/filebuf.h:904:3: warning: Member variable 'AsyncData::cur' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:43:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:43:2: warning: Member variable 'Read::hitset' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:45:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:45:2: warning: Member variable 'Read::hitset' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:342:2: warning: Member variable 'PerReadMetrics::tz_beg' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:342:2: warning: Member variable 'PerReadMetrics::seedPctUniqueMS' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:342:2: warning: Member variable 'PerReadMetrics::seedPctRepMS' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:342:2: warning: Member variable 'PerReadMetrics::seedHitAvgMS' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:342:2: warning: Member variable 'PerReadMetrics::seedsPerNucMS' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/read.h:342:2: warning: Member variable 'PerReadMetrics::maxDPFails' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1619:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1619:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1630:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1630:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1655:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1655:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1667:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1667:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1679:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1679:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::cs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::printcs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zero_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::zeroT_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::len_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::sz_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1619:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1619:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1630:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1630:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1655:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1655:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1667:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1667:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1679:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1679:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::cs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::printcs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zero_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::zeroT_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::len_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::sz_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < uint8_t * , 128 >::cat_' is not assigned a value in 'EList < uint8_t * , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < FmStringOp , 128 >::cat_' is not assigned a value in 'EList < FmStringOp , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:4196:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4196:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4221:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4221:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4221:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4246:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4246:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4246:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/ds.h:4246:43: performance: Variable 'd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/bt2_locks.h:57:7: performance:inconclusive: Technically the member function 'mcs_lock::spin_while_eq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/bt2_locks.h:63:7: performance:inconclusive: Technically the member function 'mcs_lock::spin_while_eq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:59:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
bowtie2-2.5.4/ds.h:65:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
bowtie2-2.5.4/ds.h:70:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
bowtie2-2.5.4/ds.h:76:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
bowtie2-2.5.4/ds.h:1202:29: performance:inconclusive: Technically the member function 'ELList::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:1542:34: performance:inconclusive: Technically the member function 'ELLList::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:2231:24: performance:inconclusive: Technically the member function 'ELSet::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:3127:7: performance:inconclusive: Technically the member function 'Pool::free' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sstring.h:732:7: style:inconclusive: Technically the member function 'SString::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:739:7: style:inconclusive: Technically the member function 'SString::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:746:7: style:inconclusive: Technically the member function 'SString::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:753:7: style:inconclusive: Technically the member function 'SString::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:760:7: style:inconclusive: Technically the member function 'SString::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:767:7: style:inconclusive: Technically the member function 'SString::operator>=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1380:7: style:inconclusive: Technically the member function 'S2bDnaString::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1387:7: style:inconclusive: Technically the member function 'S2bDnaString::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1394:7: style:inconclusive: Technically the member function 'S2bDnaString::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1401:7: style:inconclusive: Technically the member function 'S2bDnaString::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1408:7: style:inconclusive: Technically the member function 'S2bDnaString::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1415:7: style:inconclusive: Technically the member function 'S2bDnaString::operator>=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:2328:7: style:inconclusive: Technically the member function 'SStringFixed::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:2335:7: style:inconclusive: Technically the member function 'SStringFixed::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:2342:7: style:inconclusive: Technically the member function 'SStringFixed::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:2349:7: style:inconclusive: Technically the member function 'SStringFixed::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:2356:7: style:inconclusive: Technically the member function 'SStringFixed::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:2363:7: style:inconclusive: Technically the member function 'SStringFixed::operator>=' can be const. [functionConst]
bowtie2-2.5.4/filebuf.h:110:7: style:inconclusive: Technically the member function 'FileBuf::isOpen' can be const. [functionConst]
bowtie2-2.5.4/filebuf.h:152:7: style:inconclusive: Technically the member function 'FileBuf::eof' can be const. [functionConst]
bowtie2-2.5.4/filebuf.h:811:14: style:inconclusive: Technically the member function 'OutFileBuf::name' can be const. [functionConst]
bowtie2-2.5.4/aligner_cache.h:320:7: style:inconclusive: Technically the member function 'SAVal::valid' can be const. [functionConst]
bowtie2-2.5.4/aligner_cache.h:967:24: style:inconclusive: Technically the member function 'AlignmentCacheIface::current' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1861:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 0 >::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1868:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 0 >::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1875:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 0 >::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1882:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 0 >::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1889:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 0 >::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1896:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 0 >::operator>=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1861:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 1024 >::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1868:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 1024 >::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1875:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 1024 >::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1882:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 1024 >::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1889:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 1024 >::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1896:7: style:inconclusive: Technically the member function 'SStringExpandable < char , 1024 , 2 , 1024 >::operator>=' can be const. [functionConst]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint8_t * , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < FmStringOp , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:116:3: warning: Class 'AutoArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/ds.h:3079:3: warning: Class 'Pool' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie2-2.5.4/ds.h:3079:3: warning: Class 'Pool' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/filebuf.h:671:3: warning: Class 'OutFileBuf' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie2-2.5.4/filebuf.h:671:3: warning: Class 'OutFileBuf' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/sstring.h:684:15: style: Virtual function 'install' is called from constructor 'SString(const std::basic_string<T>&str)' at line 540. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:540:3: note: Calling install
bowtie2-2.5.4/sstring.h:684:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:684:15: style: Virtual function 'install' is called from constructor 'SString(const T*b,long sz)' at line 551. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:551:3: note: Calling install
bowtie2-2.5.4/sstring.h:684:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:684:15: style: Virtual function 'install' is called from constructor 'SString(const T*b)' at line 562. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:562:3: note: Calling install
bowtie2-2.5.4/sstring.h:684:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2290:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const std::basic_string<T>&str)' at line 2147. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2147:3: note: Calling install
bowtie2-2.5.4/sstring.h:2290:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2290:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b,long sz)' at line 2154. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2154:3: note: Calling install
bowtie2-2.5.4/sstring.h:2290:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2290:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b)' at line 2161. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2161:3: note: Calling install
bowtie2-2.5.4/sstring.h:2290:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2684:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2594. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2594:5: note: Calling installColors
bowtie2-2.5.4/sstring.h:2684:15: note: installColors is a virtual function
bowtie2-2.5.4/sstring.h:2669:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2596. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2596:5: note: Calling installChars
bowtie2-2.5.4/sstring.h:2669:15: note: installChars is a virtual function
bowtie2-2.5.4/sstring.h:2653:15: style: Virtual function 'install' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2599. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2599:4: note: Calling install
bowtie2-2.5.4/sstring.h:2653:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:3230:15: style: Virtual function 'installChars' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3154. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:3154:4: note: Calling installChars
bowtie2-2.5.4/sstring.h:3230:15: note: installChars is a virtual function
bowtie2-2.5.4/sstring.h:3214:15: style: Virtual function 'install' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3156. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:3156:4: note: Calling install
bowtie2-2.5.4/sstring.h:3214:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:3008:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2846. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2846:5: note: Calling installColors
bowtie2-2.5.4/sstring.h:3008:15: note: installColors is a virtual function
bowtie2-2.5.4/sstring.h:3000:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2848. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2848:5: note: Calling installChars
bowtie2-2.5.4/sstring.h:3000:15: note: installChars is a virtual function
bowtie2-2.5.4/sstring.h:2938:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2851. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2851:4: note: Calling install
bowtie2-2.5.4/sstring.h:2938:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2986:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2867. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2867:5: note: Calling installColors
bowtie2-2.5.4/sstring.h:2986:15: note: installColors is a virtual function
bowtie2-2.5.4/sstring.h:2972:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2869. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2869:5: note: Calling installChars
bowtie2-2.5.4/sstring.h:2972:15: note: installChars is a virtual function
bowtie2-2.5.4/sstring.h:2957:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2872. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2872:4: note: Calling install
bowtie2-2.5.4/sstring.h:2957:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2938:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,bool chars=false,bool colors=false)' at line 2885. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2885:3: note: Calling install
bowtie2-2.5.4/sstring.h:2938:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 , 0 >(const std::basic_string<char>&str)' at line 1661. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1661:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 , 0 >(const char*b,long sz)' at line 1673. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1673:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 , 0 >(const char*b)' at line 1685. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1685:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 , 1024 >(const std::basic_string<char>&str)' at line 1661. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1661:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 , 1024 >(const char*b,long sz)' at line 1673. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1673:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 , 1024 >(const char*b)' at line 1685. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1685:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2714:7: warning: The class 'SDnaStringFixed' defines member function with name 'set' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:2262:7: note: Parent function 'SStringFixed::set'
bowtie2-2.5.4/sstring.h:2714:7: note: Derived function 'SDnaStringFixed::set'
bowtie2-2.5.4/sstring.h:2761:14: warning: The class 'SDnaStringFixed' defines member function with name 'operator[]' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:2169:18: note: Parent function 'SStringFixed::operator[]'
bowtie2-2.5.4/sstring.h:2761:14: note: Derived function 'SDnaStringFixed::operator[]'
bowtie2-2.5.4/sstring.h:2768:14: warning: The class 'SDnaStringFixed' defines member function with name 'get' also defined in its parent class 'SStringFixed'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:2183:18: note: Parent function 'SStringFixed::get'
bowtie2-2.5.4/sstring.h:2768:14: note: Derived function 'SDnaStringFixed::get'
bowtie2-2.5.4/assert_helpers.h:33:2: style: Class 'ReleaseAssertException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/threading.h:70:2: style: Class 'ThreadSafe' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/random_source.h:41:2: style: Class 'RandomSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:114:2: style: Class 'AutoArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1716:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1733:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:2411:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:2426:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:71:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:77:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:90:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:96:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:563:2: style: Class 'BitpairOutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:633:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:651:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/filebuf.h:904:3: style: Class 'AsyncData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/sstring.h:1642:2: style: Class 'SStringExpandable < char , 1024 , 2 , 0 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/sstring.h:1642:2: style: Class 'SStringExpandable < char , 1024 , 2 , 1024 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:3772:2: style: Class 'RedBlack < QKey , QVal >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:3772:2: style: Class 'RedBlack < QKey , SAVal >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:3165:2: style: Class 'PList < QKey , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:3165:2: style: Class 'PList < uint32_t , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/sstring.h:2603:11: style: The destructor '~SDnaStringFixed' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/sstring.h:2164:11: note: Virtual destructor in base class
bowtie2-2.5.4/sstring.h:2603:11: note: Destructor in derived class
bowtie2-2.5.4/filebuf.h:615:11: style: Class 'BitpairOutFileBuf' is unsafe, 'BitpairOutFileBuf::out_' can leak by wrong usage. [unsafeClassCanLeak]
bowtie2-2.5.4/sstring.h:88:18: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/filebuf.h:280:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/filebuf.h:283:29: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/filebuf.h:285:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/filebuf.h:586:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/filebuf.h:606:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/filebuf.h:959:52: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/ds.h:4140:14: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/ds.h:3372:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/ds.h:603:3: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/sstring.h:3381:46: warning: Either the condition '(poss)>(0)' is redundant or there is division by zero at line 3381. [zerodivcond]
bowtie2-2.5.4/sstring.h:3380:3: note: Assuming that condition '(poss)>(0)' is not redundant
bowtie2-2.5.4/sstring.h:3381:46: note: Division by zero
bowtie2-2.5.4/filebuf.h:580:21: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
bowtie2-2.5.4/ds.h:3215:14: style: Local variable 'i' shadows outer argument [shadowArgument]
bowtie2-2.5.4/ds.h:3211:10: note: Shadowed declaration
bowtie2-2.5.4/ds.h:3215:14: note: Shadow variable
bowtie2-2.5.4/aligner_cache.h:793:9: style: Parameter 'qv' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_cache.h:830:9: style: Variable 'qv' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/ds.h:3696:34: style: Parameter 'ol' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/endian_swap.h:137:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/word_io.h:48:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/word_io.h:59:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/word_io.h:68:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/word_io.h:89:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/word_io.h:124:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/word_io.h:160:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/word_io.h:195:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ref_read.h:82:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ref_read.h:167:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sequence_io.h:45:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sequence_io.h:75:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/timer.h:141:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/timer.h:165:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/reference.h:132:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:105:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:209:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:236:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:275:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:365:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:455:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:574:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:660:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:749:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:774:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:901:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:939:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:992:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.cpp:1063:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.h:287:26: warning: Either the condition '(q)>=0' is redundant or the array 'mmpens[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
bowtie2-2.5.4/scoring.h:286:3: note: Assuming that condition '(q)>=0' is not redundant
bowtie2-2.5.4/scoring.h:287:26: note: Negative array index
bowtie2-2.5.4/scoring.h:304:43: warning: Either the condition '(q)>=0' is redundant or the array 'matchBonuses[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
bowtie2-2.5.4/scoring.h:303:3: note: Assuming that condition '(q)>=0' is not redundant
bowtie2-2.5.4/scoring.h:304:43: note: Negative array index
bowtie2-2.5.4/scoring.h:331:25: warning: Either the condition '(q)>=0' is redundant or the array 'npens[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
bowtie2-2.5.4/scoring.h:330:3: note: Assuming that condition '(q)>=0' is not redundant
bowtie2-2.5.4/scoring.h:331:25: note: Negative array index
bowtie2-2.5.4/mask.h:64:31: warning: Either the condition 'mask<32' is redundant or the array 'alts5[32]' is accessed at index 32, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie2-2.5.4/mask.h:63:2: note: Assuming that condition 'mask<32' is not redundant
bowtie2-2.5.4/mask.h:64:31: note: Array index out of bounds
bowtie2-2.5.4/mask.h:66:2: warning: Either the condition 'mask<32' is redundant or the array 'alts5[32]' is accessed at index 32, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie2-2.5.4/mask.h:63:2: note: Assuming that condition 'mask<32' is not redundant
bowtie2-2.5.4/mask.h:66:2: note: Array index out of bounds
bowtie2-2.5.4/ds.h:534:3: error: Using 'memset' on class that contains a virtual function. [memsetClass]
bowtie2-2.5.4/ds.h:541:3: error: Using 'memset' on class that contains a virtual function. [memsetClass]
bowtie2-2.5.4/scoring.h:136:2: warning: Member variable 'Scoring::matchBonuses' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/scoring.h:136:2: warning: Member variable 'Scoring::mmpens' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/scoring.h:136:2: warning: Member variable 'Scoring::npens' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/dp_framer.h:61:2: warning: Member variable 'DPRect::refl_pretrim' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/dp_framer.h:61:2: warning: Member variable 'DPRect::refr_pretrim' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/dp_framer.h:61:2: warning: Member variable 'DPRect::maxgap' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::sortedSel_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::cur_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nmm_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nnmm_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdop_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfop_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdex_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfex_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nmmPrune_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nnmmPrune_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdopPrune_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfopPrune_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdexPrune_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfexPrune_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::row_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::col_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::inited_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::nrow_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::ncol_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::nvecrow_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::nveccol_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::wperv_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::vecshift_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::nvecPerCol_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::colstride_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:107:2: warning: Member variable 'SSEMatrix::rowstride_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:408:2: warning: Member variable 'SSEData::qprofStride_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:408:2: warning: Member variable 'SSEData::gbarStride_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:408:2: warning: Member variable 'SSEData::maxPen_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:408:2: warning: Member variable 'SSEData::maxBonus_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:408:2: warning: Member variable 'SSEData::lastIter_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:408:2: warning: Member variable 'SSEData::lastWord_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_swsse.h:408:2: warning: Member variable 'SSEData::bias_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1619:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1619:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1630:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1630:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1655:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1655:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1667:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1667:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1679:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1679:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::cs_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::printcs_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zero_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::zeroT_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::len_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::sz_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:1763:8: warning: Member variable 'ESet < RedundantCell >::cat_' is not assigned a value in 'ESet < RedundantCell >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:1763:8: warning: Member variable 'ESet < unsigned long >::cat_' is not assigned a value in 'ESet < unsigned long >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < Edit , 128 >::cat_' is not assigned a value in 'EList < Edit , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < char , 128 >::cat_' is not assigned a value in 'EList < char , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < unsigned long , 128 >::cat_' is not assigned a value in 'EList < unsigned long , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < bool , 128 >::cat_' is not assigned a value in 'EList < bool , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < ESet < RedundantCell > , 128 >::cat_' is not assigned a value in 'EList < ESet < RedundantCell > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < AlnRes , 128 >::cat_' is not assigned a value in 'EList < AlnRes , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < CpQuad , 128 >::cat_' is not assigned a value in 'EList < CpQuad , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: pair < int64_t , unsigned long > , 128 >::cat_' is not assigned a value in 'EList < std :: pair < int64_t , unsigned long > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < BtBranch , 128 >::cat_' is not assigned a value in 'EList < BtBranch , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: pair < unsigned long , unsigned long > , 128 >::cat_' is not assigned a value in 'EList < std :: pair < unsigned long , unsigned long > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < uint16_t , 128 >::cat_' is not assigned a value in 'EList < uint16_t , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/scoring.h:157:3: performance: Variable 'scoreMin' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/scoring.h:158:3: performance: Variable 'nCeil' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/aligner_result.h:1819:7: performance:inconclusive: Technically the member function 'AlnSetSumm::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/dp_framer.h:118:7: style:inconclusive: Technically the member function 'DPRect::initIval' can be const. [functionConst]
bowtie2-2.5.4/dp_framer.h:246:7: performance:inconclusive: Technically the member function 'DynProgFramer::trimToRef' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sstring.h:1861:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1868:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1875:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1882:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1889:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1896:7: style:inconclusive: Technically the member function 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator>=' can be const. [functionConst]
bowtie2-2.5.4/ds.h:2231:24: performance:inconclusive: Technically the member function 'ELSet < unsigned long , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:1202:29: performance:inconclusive: Technically the member function 'ELList < std :: pair < unsigned long , unsigned long > , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:1202:29: performance:inconclusive: Technically the member function 'ELList < CpQuad , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:1202:29: performance:inconclusive: Technically the member function 'ELList < uint16_t , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Edit , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < char , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < unsigned long , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < bool , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < ESet < RedundantCell > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < ESet < RedundantCell > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < AlnRes , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < AlnRes , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < CpQuad , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < CpQuad , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: pair < int64_t , unsigned long > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: pair < int64_t , unsigned long > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < BtBranch , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < BtBranch , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: pair < unsigned long , unsigned long > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: pair < unsigned long , unsigned long > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint16_t , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < uint16_t , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 , 0 >(const std::basic_string<std::uint32_t>&str)' at line 1661. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1661:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 , 0 >(const uint32_t*b,long sz)' at line 1673. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1673:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 , 0 >(const uint32_t*b)' at line 1685. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1685:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/ds.h:3165:2: style: Class 'PList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:3772:2: style: Class 'RedBlack' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_result.h:1661:2: style: Class 'RedundantAlns' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/dp_framer.h:61:2: style: Struct 'DPRect' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/dp_framer.h:132:2: style: Class 'DynProgFramer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_swsse.h:107:2: style: Struct 'SSEMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_swsse.h:408:2: style: Struct 'SSEData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/sstring.h:1642:2: style: Class 'SStringExpandable < uint32_t , 1024 , 2 , 0 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1716:2: style: Class 'ESet < RedundantCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1733:2: style: Class 'ESet < RedundantCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1716:2: style: Class 'ESet < unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1733:2: style: Class 'ESet < unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_result.h:994:21: performance: Function 'score()' should return member 'score_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:995:21: performance: Function 'oscore()' should return member 'oscore_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1832:11: performance: Function 'bestUScore()' should return member 'bestUScore_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1833:11: performance: Function 'bestP1Score()' should return member 'bestP1Score_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1834:11: performance: Function 'bestP2Score()' should return member 'bestP2Score_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1835:11: performance: Function 'bestCScore()' should return member 'bestCScore_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1836:11: performance: Function 'bestUDist()' should return member 'bestUDist_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1837:11: performance: Function 'bestP1Dist()' should return member 'bestP1Dist_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1838:11: performance: Function 'bestP2Dist()' should return member 'bestP2Dist_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1839:11: performance: Function 'bestCDist()' should return member 'bestCDist_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1841:11: performance: Function 'bestUnchosenUScore()' should return member 'bestUnchosenUScore_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1842:11: performance: Function 'bestUnchosenP1Score()' should return member 'bestUnchosenP1Score_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1843:11: performance: Function 'bestUnchosenP2Score()' should return member 'bestUnchosenP2Score_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1844:11: performance: Function 'bestUnchosenCScore()' should return member 'bestUnchosenCScore_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1845:11: performance: Function 'bestUnchosenUDist()' should return member 'bestUnchosenUDist_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1846:11: performance: Function 'bestUnchosenP1Dist()' should return member 'bestUnchosenP1Dist_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1847:11: performance: Function 'bestUnchosenP2Dist()' should return member 'bestUnchosenP2Dist_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_result.h:1848:11: performance: Function 'bestUnchosenCDist()' should return member 'bestUnchosenCDist_' by const reference. [returnByReference]
bowtie2-2.5.4/random_util.h:130:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bitpack.h:32:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bitpack.h:38:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bitpack.h:43:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bitpack.h:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:38:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:48:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:106:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:124:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:157:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:267:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:306:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:324:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:350:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:412:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:493:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:527:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:656:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:680:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:711:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:776:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:808:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:901:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:1049:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/multikey_qsort.h:1146:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:87:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:127:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:170:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:297:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:336:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:399:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:423:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:435:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/binary_sa_search.h:56:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/zbox.h:41:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:556:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:814:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:876:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:210:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:226:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:294:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:335:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:460:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:621:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:675:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:890:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:998:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1217:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1305:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1381:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1436:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1483:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1546:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1573:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1595:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1636:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1661:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1764:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1811:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:1900:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2093:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2141:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2186:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2280:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2322:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2350:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2384:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2429:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2461:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2479:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2570:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2634:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2673:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2705:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:2840:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.h:3194:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:319:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:536:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:650:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:947:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1227:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1275:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1426:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1498:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1635:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1676:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1689:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1917:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1939:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:1970:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:2159:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable botf [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:2199:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:2418:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.h:2505:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/unique.h:65:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/unique.h:124:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/unique.h:198:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/unique.h:442:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sam.h:159:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sam.h:167:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sam.h:471:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.h:248:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.h:278:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.h:510:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.h:535:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.h:694:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.h:1055:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_driver.h:198:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_driver.cpp:30:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_driver.cpp:305:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:1174:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:1229:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:463:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:498:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:727:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:748:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:759:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:780:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:795:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:806:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:844:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:878:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:395:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:404:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:412:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:317:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:406:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:458:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:524:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:632:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:835:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:908:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:1011:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:113:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:470:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:531:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:573:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:614:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:746:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:920:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:931:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:950:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:993:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/blockwise_sa.h:607:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:721:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_result.h:1293:8: style: Condition 'sameChr' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_result.h:1292:19: note: Assignment 'sameChr=true', assigned value is 1
bowtie2-2.5.4/aligner_result.h:1293:8: note: Condition 'sameChr' is always true
bowtie2-2.5.4/qual.h:116:10: style: Condition 'cc<33' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/qual.h:115:40: note: Assignment 'cc=solexaToPhred((int)c-64)+33', assigned value is greater than 32
bowtie2-2.5.4/qual.h:116:10: note: Condition 'cc<33' is always false
bowtie2-2.5.4/scoring.h:168:28: style: Condition 'matchType==COST_MODEL_CONSTANT' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/scoring.h:152:18: note: Assignment 'matchType=COST_MODEL_CONSTANT', assigned value is 3
bowtie2-2.5.4/scoring.h:168:28: note: Condition 'matchType==COST_MODEL_CONSTANT' is always true
bowtie2-2.5.4/sse_util.h:396:6: style: Condition 'debug_' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/sse_util.h:380:12: note: Assignment 'debug_=true', assigned value is 1
bowtie2-2.5.4/sse_util.h:396:6: note: Condition 'debug_' is always true
bowtie2-2.5.4/aligner_bt.cpp:1333:7: style: Condition 'prune' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_bt.cpp:1323:17: note: Assignment 'prune=false', assigned value is 0
bowtie2-2.5.4/aligner_bt.cpp:1333:7: note: Condition 'prune' is always false
bowtie2-2.5.4/aligner_bt.cpp:1529:17: style: Condition 'hi-lo<hi_sm-lo_sm' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_bt.cpp:1516:13: note: Assuming that condition 'newhi>newlo' is not redundant
bowtie2-2.5.4/aligner_bt.cpp:1528:19: note: lo_sm is assigned 'newlo' here.
bowtie2-2.5.4/aligner_bt.cpp:1528:36: note: Assignment 'hi_sm=newhi', assigned value is less than symbolic=lo_sm
bowtie2-2.5.4/aligner_bt.cpp:1529:17: note: Condition 'hi-lo<hi_sm-lo_sm' is always false
bowtie2-2.5.4/sse_util.h:420:25: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/sse_util.h:497:25: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse.h:232:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse.h:235:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_bt.cpp:705:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_bt.cpp:706:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_bt.cpp:717:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_bt.cpp:718:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/sse_util.h:427:17: style: Variable 'asc' is assigned an expression that holds the same value. [redundantAssignment]
bowtie2-2.5.4/sse_util.h:421:15: note: asc is assigned 'MIN_I64' here.
bowtie2-2.5.4/sse_util.h:427:17: note: Variable 'asc' is assigned an expression that holds the same value.
bowtie2-2.5.4/sse_util.h:504:17: style: Variable 'asc' is assigned an expression that holds the same value. [redundantAssignment]
bowtie2-2.5.4/sse_util.h:498:15: note: asc is assigned 'MIN_I64' here.
bowtie2-2.5.4/sse_util.h:504:17: note: Variable 'asc' is assigned an expression that holds the same value.
bowtie2-2.5.4/mask.h:76:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bowtie2-2.5.4/aligner_bt.cpp:648:9: style: The scope of the variable 'xi' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_bt.cpp:1171:9: style: The scope of the variable 'iters' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_bt.cpp:697:25: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:697:25: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:727:5: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:727:5: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:728:5: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:728:5: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:756:7: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:756:7: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:761:7: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:761:7: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:853:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:853:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:854:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:854:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:855:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_bt.cpp:855:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/sse_util.h:218:12: style: Local variable 'last_alloc_' shadows outer variable [shadowVariable]
bowtie2-2.5.4/sse_util.h:324:11: note: Shadowed declaration
bowtie2-2.5.4/sse_util.h:218:12: note: Shadow variable
bowtie2-2.5.4/aligner_bt.h:736:12: style: Local variable 'row' shadows outer argument [shadowArgument]
bowtie2-2.5.4/aligner_bt.h:687:18: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.h:736:12: note: Shadow variable
bowtie2-2.5.4/aligner_bt.h:736:24: style: Local variable 'col' shadows outer argument [shadowArgument]
bowtie2-2.5.4/aligner_bt.h:688:18: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.h:736:24: note: Shadow variable
bowtie2-2.5.4/aligner_bt.cpp:357:10: style: Local variable 'mod' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_bt.cpp:69:9: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.cpp:357:10: note: Shadow variable
bowtie2-2.5.4/aligner_bt.cpp:421:10: style: Local variable 'empty' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_bt.h:602:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.cpp:421:10: note: Shadow variable
bowtie2-2.5.4/aligner_bt.cpp:532:11: style: Local variable 'cur' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_bt.cpp:359:12: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.cpp:532:11: note: Shadow variable
bowtie2-2.5.4/aligner_bt.cpp:964:10: style: Local variable 'empty' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_bt.h:602:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.cpp:964:10: note: Shadow variable
bowtie2-2.5.4/aligner_bt.cpp:1077:11: style: Local variable 'cur' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_bt.cpp:904:12: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.cpp:1077:11: note: Shadow variable
bowtie2-2.5.4/aligner_bt.cpp:1178:9: style: Local variable 'matches' shadows outer function [shadowFunction]
bowtie2-2.5.4/mask.h:48:20: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.cpp:1178:9: note: Shadow variable
bowtie2-2.5.4/aligner_bt.cpp:1488:11: style: Local variable 'diag' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_bt.cpp:1477:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_bt.cpp:1488:11: note: Shadow variable
bowtie2-2.5.4/aligner_result.h:951:25: performance: Function parameter 'score' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1910:12: performance: Function parameter 'bestUScore' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1911:12: performance: Function parameter 'bestUDist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1912:12: performance: Function parameter 'bestP1Score' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1913:12: performance: Function parameter 'bestP1Dist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1914:12: performance: Function parameter 'bestP2Score' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1915:12: performance: Function parameter 'bestP2Dist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1916:12: performance: Function parameter 'bestCScore' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1917:12: performance: Function parameter 'bestCDist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1918:12: performance: Function parameter 'bestUnchosenUScore' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1919:12: performance: Function parameter 'bestUnchosenUDist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1920:12: performance: Function parameter 'bestUnchosenP1Score' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1921:12: performance: Function parameter 'bestUnchosenP1Dist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1922:12: performance: Function parameter 'bestUnchosenP2Score' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1923:12: performance: Function parameter 'bestUnchosenP2Dist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1924:12: performance: Function parameter 'bestUnchosenCScore' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.h:1925:12: performance: Function parameter 'bestUnchosenCDist' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/dp_framer.h:248:12: style: Parameter 'refl' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/dp_framer.h:249:12: style: Parameter 'refr' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_bt.h:589:28: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_bt.cpp:46:16: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_bt.cpp:596:16: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_bt.cpp:1241:12: style: Variable 'b' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_bt.cpp:1698:10: style: Parameter 'niter' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_bt.cpp:516:12: style: Variable 'cur_new' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/aligner_bt.cpp:1062:12: style: Variable 'cur_new' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/timer.h:157:12: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
bowtie2-2.5.4/ref_read.h:219:3: 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]
bowtie2-2.5.4/ref_read.h:172:2: note: Assuming that condition '-1!=(lastc)' is not redundant
bowtie2-2.5.4/ref_read.h:184:4: note: c is assigned 'lastc' here.
bowtie2-2.5.4/ref_read.h:219:3: note: Invalid argument
bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString < char >::cs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString < char >::printcs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString < char >::len_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < FileBuf * , 128 >::cat_' is not assigned a value in 'EList < FileBuf * , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < RefRecord , 128 >::cat_' is not assigned a value in 'EList < RefRecord , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < string , 128 >::cat_' is not assigned a value in 'EList < string , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < SString < char > , 128 >::cat_' is not assigned a value in 'EList < SString < char > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < uint32_t , 128 >::cat_' is not assigned a value in 'EList < uint32_t , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ref_read.h:48:3: performance: Variable 'msg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/timer.h:131:7: style:inconclusive: Technically the member function 'Timer::write' can be const. [functionConst]
bowtie2-2.5.4/aligner_result.h:1043:8: performance:inconclusive: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_result.cpp:913:14: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/aligner_result.h:1043:8: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sstring.h:732:7: style:inconclusive: Technically the member function 'SString < char >::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:739:7: style:inconclusive: Technically the member function 'SString < char >::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:746:7: style:inconclusive: Technically the member function 'SString < char >::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:753:7: style:inconclusive: Technically the member function 'SString < char >::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:760:7: style:inconclusive: Technically the member function 'SString < char >::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:767:7: style:inconclusive: Technically the member function 'SString < char >::operator>=' can be const. [functionConst]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < FileBuf * , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < RefRecord , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < string , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SString < char > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint32_t , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/sstring.h:684:15: style: Virtual function 'install' is called from constructor 'SString < char >(const std::basic_string<char>&str)' at line 540. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:540:3: note: Calling install
bowtie2-2.5.4/sstring.h:684:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:684:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b,long sz)' at line 551. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:551:3: note: Calling install
bowtie2-2.5.4/sstring.h:684:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:684:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b)' at line 562. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:562:3: note: Calling install
bowtie2-2.5.4/sstring.h:684:15: note: install is a virtual function
bowtie2-2.5.4/timer.h:118:2: style: Class 'Timer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ref_read.h:288:14: style: Expression is always true because 'else if' condition is opposite to previous condition at line 286. [multiCondition]
bowtie2-2.5.4/ref_read.h:286:13: note: first condition
bowtie2-2.5.4/ref_read.h:288:14: note: else if condition is opposite to first condition
bowtie2-2.5.4/endian_swap.h:40:11: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:48:13: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:59:13: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:68:13: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:89:10: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:124:11: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:160:10: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:195:11: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/word_io.h:39:13: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_bt.cpp:648:12: style: Variable 'xi' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_bt.cpp:671:20: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_bt.cpp:671:39: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_result.cpp:931:31: style: The scope of the variable 'right' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_result.cpp:982:31: style: The scope of the variable 'right' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_result.cpp:209:2: style: Unsigned expression 'rd_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_result.cpp:210:2: style: Unsigned expression 'rf_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_result.cpp:236:2: style: Unsigned expression 'rd_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_result.cpp:237:2: style: Unsigned expression 'rf_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_result.cpp:770:8: style:inconclusive: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_result.h:716:37: note: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'.
bowtie2-2.5.4/aligner_result.cpp:770:8: note: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'.
bowtie2-2.5.4/aligner_result.cpp:805:46: style:inconclusive: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_result.h:722:35: note: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'.
bowtie2-2.5.4/aligner_result.cpp:805:46: note: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'.
bowtie2-2.5.4/aligner_result.cpp:446:7: style: Local variable 'fw' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_result.h:990:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_result.cpp:446:7: note: Shadow variable
bowtie2-2.5.4/aligner_result.cpp:1058:7: style: Local variable 'paired' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_result.h:1826:11: note: Shadowed declaration
bowtie2-2.5.4/aligner_result.cpp:1058:7: note: Shadow variable
bowtie2-2.5.4/aligner_result.cpp:129:21: performance: Function parameter 'score' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.cpp:136:21: performance: Function parameter 'refcoord' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_result.cpp:438:12: style: Parameter 'qseq' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_result.cpp:463:8: style: Variable 'refbuf' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/aligner_result.cpp:788:6: style: Variable 'bufc' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/aligner_result.cpp:820:23: style: Variable 'bufc' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/timer.h:154:13: style: Variable 'current' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/ds.h:4167:14: debug: Failed to instantiate template "EList". The checking continues anyway. [templateInstantiation]
bowtie2-2.5.4/aligner_seed.h:163:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:176:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:205:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:578:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:654:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:694:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:952:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:961:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:988:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:1068:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:1112:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:1156:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:1179:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:1188:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.h:1228:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:101:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:231:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:513:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:659:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:738:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:763:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:867:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:998:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:1380:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:1480:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:1622:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:1640:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:1773:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:1895:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:63:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:155:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pen [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:236:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:348:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gapadd_ [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:445:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off5p [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:546:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:894:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:1000:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:1079:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:1263:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:1342:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_driver.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie2-2.5.4/aligner_seed2.h:540:15: warning: Assert statement calls a function which may have desired side effects: 'containsEx'. [assertWithSideEffect]
bowtie2-2.5.4/aligner_driver.cpp:336:18: warning: Assert statement calls a function which may have desired side effects: 'matchesRef'. [assertWithSideEffect]
bowtie2-2.5.4/multikey_qsort.h:1079:21: warning: Either the condition '(c)<=4' is redundant or the array 'bkts[4]' is accessed at index 4, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie2-2.5.4/multikey_qsort.h:1075:13: note: Assuming that condition '(c)<=4' is not redundant
bowtie2-2.5.4/multikey_qsort.h:1079:21: note: Array index out of bounds
bowtie2-2.5.4/multikey_qsort.h:1079:31: warning: Either the condition '(c)<=4' is redundant or the array 'cnts[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
bowtie2-2.5.4/multikey_qsort.h:1075:13: note: Assuming that condition '(c)<=4' is not redundant
bowtie2-2.5.4/multikey_qsort.h:1079:31: note: Array index out of bounds
bowtie2-2.5.4/ds.h:534:3: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
bowtie2-2.5.4/ds.h:541:3: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
bowtie2-2.5.4/random_util.h:50:2: warning: Member variable 'Random1toN::swaplist_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/random_util.h:50:2: warning: Member variable 'Random1toN::converted_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/random_util.h:55:2: warning: Member variable 'Random1toN::swaplist_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/random_util.h:55:2: warning: Member variable 'Random1toN::converted_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_len' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_bwtLen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_sz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_bwtSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_lineRate' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_offRate' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_offMask' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_eftabLen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_eftabSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_ftabLen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_ftabSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_offsLen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_offsSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_lineSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_sideSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_sideBwtSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_sideBwtLen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_numSides' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_numLines' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_ebwtTotLen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_ebwtTotSz' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_color' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_idx.h:115:2: warning:inconclusive: Member variable 'EbwtParams::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::pen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::depth' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::rootpri' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:621:2: warning: Member variable 'DescentRoot::l2r' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:621:2: warning: Member variable 'DescentRoot::fw' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:621:2: warning: Member variable 'DescentRoot::landing' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:621:2: warning: Member variable 'DescentRoot::pri' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::nex' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::posFlag' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::d' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::topf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::botf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::topb' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::botb' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:875:2: warning: Member variable 'DescentEdge::off5p' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:877:2: warning: Member variable 'DescentEdge::nex' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::rid_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::al5pi_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::al5pf_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::l2r_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::gapadd_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::off5p_i_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::topf_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::botf_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::topb_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::botb_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::parent_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::pen_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::posid_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1098:2: warning: Member variable 'Descent::len_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1867:2: warning: Member variable 'DescentDriver::minsc_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed2.h:1867:2: warning: Member variable 'DescentDriver::maxpen_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_driver.h:186:2: warning: Member variable 'AlignerDriver::paired_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > >::len' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:102:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > >::topf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:102:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > >::len' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:2451:8: warning: Member variable 'EMap < DescentRedundancyKey , int64_t >::cat_' is not assigned a value in 'EMap < DescentRedundancyKey , int64_t >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:1763:8: warning: Member variable 'ESet < Triple < uint32_t , uint32_t , unsigned long > >::cat_' is not assigned a value in 'ESet < Triple < uint32_t , uint32_t , unsigned long > >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < uint32_t , 16 >::cat_' is not assigned a value in 'EList < uint32_t , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DescentRoot , 128 >::cat_' is not assigned a value in 'EList < DescentRoot , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DescentConfig , 128 >::cat_' is not assigned a value in 'EList < DescentConfig , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DescentAlignment , 128 >::cat_' is not assigned a value in 'EList < DescentAlignment , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DescentPartialResolvedAlignment , 128 >::cat_' is not assigned a value in 'EList < DescentPartialResolvedAlignment , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < SARangeWithOffs < EListSlice < uint32_t , 16 > > , 128 >::cat_' is not assigned a value in 'EList < SARangeWithOffs < EListSlice < uint32_t , 16 > > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < GroupWalk2S < EListSlice < uint32_t , 16 > , 16 > , 128 >::cat_' is not assigned a value in 'EList < GroupWalk2S < EListSlice < uint32_t , 16 > , 16 > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: string , 128 >::cat_' is not assigned a value in 'EList < std :: string , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < SStringExpandable < char , 1024 , 2 , 0 > , 128 >::cat_' is not assigned a value in 'EList < SStringExpandable < char , 1024 , 2 , 0 > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: pair < AlnScore , unsigned long > , 128 >::cat_' is not assigned a value in 'EList < std :: pair < AlnScore , unsigned long > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < int , 128 >::cat_' is not assigned a value in 'EList < int , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < GWState < EListSlice < uint32_t , 16 > > , 16 >::cat_' is not assigned a value in 'EList < GWState < EListSlice < uint32_t , 16 > > , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: pair < uint32_t , uint32_t > , 16 >::cat_' is not assigned a value in 'EList < std :: pair < uint32_t , uint32_t > , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < bool , 16 >::cat_' is not assigned a value in 'EList < bool , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: pair < DescentPriority , unsigned long > , 128 >::cat_' is not assigned a value in 'EList < std :: pair < DescentPriority , unsigned long > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < uint8_t , 128 >::cat_' is not assigned a value in 'EList < uint8_t , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DescentPos , 128 >::cat_' is not assigned a value in 'EList < DescentPos , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < Descent , 128 >::cat_' is not assigned a value in 'EList < Descent , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < EMap < DescentRedundancyKey , int64_t > , NPARTS >::cat_' is not assigned a value in 'EList < EMap < DescentRedundancyKey , int64_t > , NPARTS >::operator='. [operatorEqVarError]
bowtie2-2.5.4/bt2_idx.h:671:3: performance: Variable '_in1Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/bt2_idx.h:672:3: performance: Variable '_in2Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/outq.h:66:3: performance: Variable 'nstarted_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/aligner_driver.h:98:3: performance: Variable 'rootIval_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/aligner_driver.h:135:3: performance: Variable 'rootIval_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bowtie2-2.5.4/threadpool.h:105:13: style:inconclusive: Technically the member function 'thread_pool::size' can be const. [functionConst]
bowtie2-2.5.4/bt2_idx.h:961:7: style:inconclusive: Technically the member function 'Ebwt::isPacked' can be const. [functionConst]
bowtie2-2.5.4/bt2_idx.h:1214:13: performance:inconclusive: Technically the member function 'Ebwt::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/bt2_idx.h:2569:11: performance:inconclusive: Technically the member function 'Ebwt::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_seed2.h:733:7: style:inconclusive: Technically the member function 'DescentPosFlags::mmExplore' can be const. [functionConst]
bowtie2-2.5.4/aligner_seed2.h:766:7: style:inconclusive: Technically the member function 'DescentPosFlags::rdgExplore' can be const. [functionConst]
bowtie2-2.5.4/aligner_seed2.h:799:7: style:inconclusive: Technically the member function 'DescentPosFlags::rfgExplore' can be const. [functionConst]
bowtie2-2.5.4/aligner_seed2.h:1257:7: style:inconclusive: Technically the member function 'Descent::collectEdits' can be const. [functionConst]
bowtie2-2.5.4/aligner_seed2.h:1937:7: style:inconclusive: Technically the member function 'DescentDriver::printRoots' can be const. [functionConst]
bowtie2-2.5.4/aligner_seed2.h:2021:7: performance:inconclusive: Technically the member function 'DescentDriver::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_seed2.h:2090:28: style:inconclusive: Technically the member function 'DescentDriver::roots' can be const. [functionConst]
bowtie2-2.5.4/aligner_seed2.h:2100:7: performance:inconclusive: Technically the member function 'DescentDriver::nextPartial' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sam.h:267:7: performance:inconclusive: Technically the member function 'SamConfig::printOptFieldEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sam.h:290:7: performance:inconclusive: Technically the member function 'SamConfig::printOptFieldNewlineEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sam.h:430:7: performance:inconclusive: Technically the member function 'SamConfig::isIllumina' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aln_sink.h:794:7: performance:inconclusive: Technically the member function 'AlnSink::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_driver.h:284:23: style:inconclusive: Technically the member function 'AlignerDriver::dr1' can be const. [functionConst]
bowtie2-2.5.4/aligner_driver.h:285:23: style:inconclusive: Technically the member function 'AlignerDriver::dr2' can be const. [functionConst]
bowtie2-2.5.4/group_walk.h:1150:7: style:inconclusive: Technically the member function 'GroupWalk2S < EListSlice < uint32_t , 16 > , 16 >::resolveAll' can be const. [functionConst]
bowtie2-2.5.4/group_walk.h:385:7: performance:inconclusive: Technically the member function 'GWHit < EListSlice < uint32_t , 16 > >::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/diff_sample.h:520:7: style:inconclusive: Technically the member function 'DifferenceCoverSample < S2bDnaString >::print' can be const. [functionConst]
bowtie2-2.5.4/threadpool.h:39:9: style:inconclusive: Technically the member function 'threadsafe_queue < std :: function < void ( ) > >::size' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:1202:29: performance:inconclusive: Technically the member function 'ELList < EMap < DescentRedundancyKey , int64_t > , NPARTS , 100 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint32_t , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < uint32_t , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DescentRoot , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DescentRoot , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DescentConfig , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DescentConfig , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DescentAlignment , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DescentAlignment , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DescentPartialResolvedAlignment , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DescentPartialResolvedAlignment , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SARangeWithOffs < EListSlice < uint32_t , 16 > > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SARangeWithOffs < EListSlice < uint32_t , 16 > > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < GroupWalk2S < EListSlice < uint32_t , 16 > , 16 > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < GroupWalk2S < EListSlice < uint32_t , 16 > , 16 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: string , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SStringExpandable < char , 1024 , 2 , 0 > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SStringExpandable < char , 1024 , 2 , 0 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: pair < AlnScore , unsigned long > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: pair < AlnScore , unsigned long > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < int , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < int , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < GWState < EListSlice < uint32_t , 16 > > , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < GWState < EListSlice < uint32_t , 16 > > , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: pair < uint32_t , uint32_t > , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: pair < uint32_t , uint32_t > , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < bool , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < bool , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: pair < DescentPriority , unsigned long > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: pair < DescentPriority , unsigned long > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < uint8_t , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DescentPos , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DescentPos , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Descent , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Descent , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < EMap < DescentRedundancyKey , int64_t > , NPARTS >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < EMap < DescentRedundancyKey , int64_t > , NPARTS >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/outq.h:70:4: warning: Class 'OutputQueue' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie2-2.5.4/outq.h:70:4: warning: Class 'OutputQueue' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/aligner_driver.h:206:4: warning: Class 'AlignerDriver' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie2-2.5.4/aligner_driver.h:206:4: warning: Class 'AlignerDriver' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/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]
bowtie2-2.5.4/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]
bowtie2-2.5.4/blockwise_sa.h:431:15: style: Virtual function 'reset' is called from constructor 'KarkkainenBlockwiseSA < S2bDnaString >(const S2bDnaString&__text,uint32_t __bucketSz,int __nthreads,thread_pool&pool,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 282. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/blockwise_sa.h:282:30: note: Calling reset
bowtie2-2.5.4/blockwise_sa.h:431:15: note: reset is a virtual function
bowtie2-2.5.4/random_util.h:50:2: style: Class 'Random1toN' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/random_util.h:55:2: style: Class 'Random1toN' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/threadpool.h:67:2: style: Class 'thread_pool' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/bt2_idx.h:285:2: style: Class 'EbwtFileOpenException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/group_walk.h:139:2: style: Struct 'GroupWalkState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_seed2.h:1867:2: style: Class 'DescentDriver' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aln_sink.h:354:2: style: Class 'ReportingState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/blockwise_sa.h:388:3: style: Class 'nextBlock_Worker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:2411:2: style: Class 'EMap < DescentRedundancyKey , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:2426:2: style: Class 'EMap < DescentRedundancyKey , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1716:2: style: Class 'ESet < Triple < uint32_t , uint32_t , unsigned long > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1733:2: style: Class 'ESet < Triple < uint32_t , uint32_t , unsigned long > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:114:2: style: Class 'AutoArray < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/blockwise_sa.h:586:2: style: Class 'BinarySorting_worker < S2bDnaString >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/diff_sample.h:703:2: style: Class 'VSorting_worker < S2bDnaString >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/unique.h:107:11: style: The destructor '~BowtieMapq3' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/unique.h:76:11: note: Virtual destructor in base class
bowtie2-2.5.4/unique.h:107:11: note: Destructor in derived class
bowtie2-2.5.4/unique.h:112:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/unique.h:78:16: note: Virtual function in base class
bowtie2-2.5.4/unique.h:112:16: note: Function in derived class
bowtie2-2.5.4/unique.h:182:11: style: The destructor '~BowtieMapq2' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/unique.h:76:11: note: Virtual destructor in base class
bowtie2-2.5.4/unique.h:182:11: note: Destructor in derived class
bowtie2-2.5.4/unique.h:187:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/unique.h:78:16: note: Virtual function in base class
bowtie2-2.5.4/unique.h:187:16: note: Function in derived class
bowtie2-2.5.4/unique.h:428:11: style: The destructor '~BowtieMapq' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/unique.h:76:11: note: Virtual destructor in base class
bowtie2-2.5.4/unique.h:428:11: note: Destructor in derived class
bowtie2-2.5.4/unique.h:433:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/unique.h:78:16: note: Virtual function in base class
bowtie2-2.5.4/unique.h:433:16: note: Function in derived class
bowtie2-2.5.4/aln_sink.h:1310:11: style: The destructor '~AlnSinkSam' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/aln_sink.h:610:11: note: Virtual destructor in base class
bowtie2-2.5.4/aln_sink.h:1310:11: note: Destructor in derived class
bowtie2-2.5.4/aln_sink.h:1318:15: style: The function 'append' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/aln_sink.h:617:15: note: Virtual function in base class
bowtie2-2.5.4/aln_sink.h:1318:15: note: Function in derived class
bowtie2-2.5.4/aligner_driver.h:102:11: style: The destructor '~IntervalRootSelector' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/aligner_seed2.h:1785:11: note: Virtual destructor in base class
bowtie2-2.5.4/aligner_driver.h:102:11: note: Destructor in derived class
bowtie2-2.5.4/aligner_driver.h:104:15: style: The function 'select' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/aligner_seed2.h:1787:15: note: Virtual function in base class
bowtie2-2.5.4/aligner_driver.h:104:15: note: Function in derived class
bowtie2-2.5.4/aligner_driver.h:139:11: style: The destructor '~PrioritizedRootSelector' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/aligner_seed2.h:1785:11: note: Virtual destructor in base class
bowtie2-2.5.4/aligner_driver.h:139:11: note: Destructor in derived class
bowtie2-2.5.4/aligner_driver.h:141:15: style: The function 'select' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/aligner_seed2.h:1787:15: note: Virtual function in base class
bowtie2-2.5.4/aligner_driver.h:141:15: note: Function in derived class
bowtie2-2.5.4/blockwise_sa.h:284:3: style: The destructor '~KarkkainenBlockwiseSA < S2bDnaString >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/blockwise_sa.h:98:11: note: Virtual destructor in base class
bowtie2-2.5.4/blockwise_sa.h:284:3: note: Destructor in derived class
bowtie2-2.5.4/blockwise_sa.h:305:21: style: The function 'nextSuffix' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/blockwise_sa.h:103:21: note: Virtual function in base class
bowtie2-2.5.4/blockwise_sa.h:305:21: note: Function in derived class
bowtie2-2.5.4/blockwise_sa.h:367:15: style: The function 'nextBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/blockwise_sa.h:159:15: note: Virtual function in base class
bowtie2-2.5.4/blockwise_sa.h:367:15: note: Function in derived class
bowtie2-2.5.4/blockwise_sa.h:373:15: style: The function 'hasMoreBlocks' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/blockwise_sa.h:161:15: note: Virtual function in base class
bowtie2-2.5.4/blockwise_sa.h:373:15: note: Function in derived class
bowtie2-2.5.4/blockwise_sa.h:431:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/blockwise_sa.h:151:15: note: Virtual function in base class
bowtie2-2.5.4/blockwise_sa.h:431:15: note: Function in derived class
bowtie2-2.5.4/blockwise_sa.h:440:15: style: The function 'isReset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/blockwise_sa.h:153:15: note: Virtual function in base class
bowtie2-2.5.4/blockwise_sa.h:440:15: note: Function in derived class
bowtie2-2.5.4/diff_sample.h:239:13: style: Condition 'keepGoing' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/diff_sample.h:210:22: note: Assignment 'keepGoing=false', assigned value is 0
bowtie2-2.5.4/diff_sample.h:239:13: note: Condition 'keepGoing' is always false
bowtie2-2.5.4/bt2_idx.h:1770:31: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/bt2_idx.h:1769:31: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie2-2.5.4/bt2_idx.h:1766:74: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie2-2.5.4/bt2_idx.h:1770:31: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie2-2.5.4/bt2_idx.h:1822:32: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/bt2_idx.h:1821:32: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie2-2.5.4/bt2_idx.h:1818:65: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie2-2.5.4/bt2_idx.h:1822:32: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie2-2.5.4/bt2_idx.h:1895:31: style: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/bt2_idx.h:1894:31: note: Assuming that condition 'l._sideByteOff+l._by>_zEbwtByteOff' is not redundant
bowtie2-2.5.4/bt2_idx.h:1891:64: note: Assuming that condition 'l._sideByteOff+l._by>=_zEbwtByteOff' is not redundant
bowtie2-2.5.4/bt2_idx.h:1895:31: note: Condition 'l._sideByteOff+l._by==_zEbwtByteOff' is always true
bowtie2-2.5.4/aligner_driver.cpp:289:39: style: Condition 'stopc1.totsz<=stop_.totsz' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_driver.cpp:288:22: note: Assuming that condition 'stopc1.totsz<=stop_.totsz' is not redundant
bowtie2-2.5.4/aligner_driver.cpp:289:39: note: Condition 'stopc1.totsz<=stop_.totsz' is always true
bowtie2-2.5.4/bt2_idx.h:1038:6: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_idx.h:2728:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_idx.h:2872:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_idx.h:2892:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_idx.h:3142:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/blockwise_sa.h:659:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/blockwise_sa.h:712:6: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/blockwise_sa.h:1045:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/blockwise_sa.h:1066:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/blockwise_sa.h:1110:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/blockwise_sa.h:1160:8: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_idx.h:942:5: error: Null pointer dereference [nullPointer]
bowtie2-2.5.4/bt2_idx.h:1953:27: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_idx.h:2062:18: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_idx.h:3080:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_seed2.h:727:11: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:320:25: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:322:38: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:390:47: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:527:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:725:32: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:727:61: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/diff_sample.h:777:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/diff_sample.h:780:33: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/diff_sample.h:827:31: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/diff_sample.h:829:58: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/diff_sample.h:890:4: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/diff_sample.h:891:4: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:588:37: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/diff_sample.h:706:33: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/blockwise_sa.h:553:9: style: The scope of the variable 'len' can be reduced. [variableScope]
bowtie2-2.5.4/unique.h:448:12: style: The scope of the variable 'secbest' can be reduced. [variableScope]
bowtie2-2.5.4/blockwise_sa.h:1026:13: style: The scope of the variable 'lo' can be reduced. [variableScope]
bowtie2-2.5.4/blockwise_sa.h:1126:11: style: The scope of the variable 'kHi' can be reduced. [variableScope]
bowtie2-2.5.4/blockwise_sa.h:1126:21: style: The scope of the variable 'kLo' can be reduced. [variableScope]
bowtie2-2.5.4/blockwise_sa.h:1127:11: style: The scope of the variable 'jHi' can be reduced. [variableScope]
bowtie2-2.5.4/blockwise_sa.h:1127:21: style: The scope of the variable 'jLo' can be reduced. [variableScope]
bowtie2-2.5.4/blockwise_sa.h:1128:8: style: The scope of the variable 'kHiSoft' can be reduced. [variableScope]
bowtie2-2.5.4/blockwise_sa.h:1128:25: style: The scope of the variable 'kLoSoft' can be reduced. [variableScope]
bowtie2-2.5.4/diff_sample.h:762:13: style: The scope of the variable 'nextRank' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:101:8: style: The scope of the variable 'pl' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:101:18: style: The scope of the variable 'pn' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:102:7: style: The scope of the variable 's' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:128:7: style: The scope of the variable 'f' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:189:18: style: The scope of the variable 'd' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:189:21: style: The scope of the variable 'g' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:288:8: style: The scope of the variable 'pi' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:289:10: style: The scope of the variable 'j' can be reduced. [variableScope]
bowtie2-2.5.4/ls.h:289:16: style: The scope of the variable 'sl' can be reduced. [variableScope]
bowtie2-2.5.4/multikey_qsort.h:928:2: style: Unsigned expression 'lim' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/unique.h:133:4: style: Unsigned expression 'best_bin' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/unique.h:139:5: style: Unsigned expression 'diff_bin' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/group_walk.h:636:3: style: Unsigned expression 'trimBegin' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/diff_sample.h:625:3: style: Unsigned expression 'sz' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/multikey_qsort.h:1022:17: style: Local variable 'bkts' shadows outer variable [shadowVariable]
bowtie2-2.5.4/multikey_qsort.h:844:19: note: Shadowed declaration
bowtie2-2.5.4/multikey_qsort.h:1022:17: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:156:16: style: Local variable 'ds' shadows outer variable [shadowVariable]
bowtie2-2.5.4/diff_sample.h:152:5: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:156:16: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:252:8: style: Local variable 'i' shadows outer argument [shadowArgument]
bowtie2-2.5.4/diff_sample.h:143:25: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:252:8: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:302:10: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/diff_sample.h:273:5: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:302:10: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:313:10: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/diff_sample.h:273:5: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:313:10: note: Shadow variable
bowtie2-2.5.4/bt2_idx.h:2837:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1242:27: note: Shadowed declaration
bowtie2-2.5.4/bt2_idx.h:2837:20: note: Shadow variable
bowtie2-2.5.4/bt2_idx.h:2849:13: style: Local variable 'fchr' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1248:23: note: Shadowed declaration
bowtie2-2.5.4/bt2_idx.h:2849:13: note: Shadow variable
bowtie2-2.5.4/bt2_idx.h:2850:20: style: Local variable 'ftab' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1249:23: note: Shadowed declaration
bowtie2-2.5.4/bt2_idx.h:2850:20: note: Shadow variable
bowtie2-2.5.4/bt2_idx.h:2851:13: style: Local variable 'zOff' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1243:16: note: Shadowed declaration
bowtie2-2.5.4/bt2_idx.h:2851:13: note: Shadow variable
bowtie2-2.5.4/bt2_idx.h:2900:7: style: Local variable 'fw' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1265:14: note: Shadowed declaration
bowtie2-2.5.4/bt2_idx.h:2900:7: note: Shadow variable
bowtie2-2.5.4/bt2_idx.h:3134:20: style: Local variable 'eftab' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1250:23: note: Shadowed declaration
bowtie2-2.5.4/bt2_idx.h:3134:20: note: Shadow variable
bowtie2-2.5.4/aligner_driver.cpp:108:14: style: Local variable 'revi' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_driver.cpp:87:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_driver.cpp:108:14: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:571:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:497:11: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:571:11: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:579:12: style: Local variable 'd' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:502:11: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:579:12: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:610:25: style: Local variable 'ds' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:506:25: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:610:25: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:612:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:497:11: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:612:11: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:613:11: style: Local variable 'd' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:502:11: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:613:11: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:749:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:497:11: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:749:11: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:986:25: style: Local variable 'dmap' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:507:25: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:986:25: note: Shadow variable
bowtie2-2.5.4/diff_sample.h:992:11: style: Local variable 'v' shadows outer function [shadowFunction]
bowtie2-2.5.4/diff_sample.h:497:11: note: Shadowed declaration
bowtie2-2.5.4/diff_sample.h:992:11: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.h:880:19: performance: Function parameter 'pri_' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_seed2.h:916:19: performance: Function parameter 'pri_' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_seed2.h:1017:26: performance: Function parameter 'e' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/ds.h:2919:16: performance: Function parameter 'o' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/bt2_idx.h:1214:41: style: Parameter 'szs' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/bt2_idx.h:1631:32: style: Parameter 'eh' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/bt2_idx.h:1805:14: style: Parameter 'l' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/bt2_idx.h:2270:14: style: Parameter 'lbot' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/bt2_idx.h:2725:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_idx.h:2868:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_idx.h:2888:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_idx.h:3138:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_seed2.h:571:39: style: Variable 'map' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_seed2.h:2407:11: style: Parameter 'rs' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_seed2.h:2495:31: style: Parameter 'pf' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/group_walk.h:1109:17: style: Parameter 'rnd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/group_walk.h:756:35: style: Parameter 'hit' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/group_walk.h:842:16: style: Parameter 'met' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/group_walk.h:325:23: style: Parameter 'sa' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/blockwise_sa.h:657:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/blockwise_sa.h:710:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/blockwise_sa.h:1043:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/blockwise_sa.h:1108:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/unique.h:62:9: style: Parameter 'inps' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/multikey_qsort.h:323:53: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/blockwise_sa.h:320:8: style: Instance of 'nextBlock_Worker' object is destroyed immediately. [unusedScopedObject]
bowtie2-2.5.4/diff_sample.h:827:8: style: Instance of 'VSorting_worker < S2bDnaString >' object is destroyed immediately. [unusedScopedObject]
bowtie2-2.5.4/bt2_idx.h:736:3: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
bowtie2-2.5.4/bt2_idx.h:747:3: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
bowtie2-2.5.4/bt2_idx.h:758:4: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
bowtie2-2.5.4/bt2_idx.h:771:4: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
bowtie2-2.5.4/bitpack.h:45:18: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 44. [shiftTooManyBits]
bowtie2-2.5.4/bitpack.h:44:2: note: Assuming that condition 'off<16' is not redundant
bowtie2-2.5.4/bitpack.h:45:18: note: Shift
bowtie2-2.5.4/bitpack.h:50:19: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 49. [shiftTooManyBits]
bowtie2-2.5.4/bitpack.h:49:2: note: Assuming that condition 'off<16' is not redundant
bowtie2-2.5.4/bitpack.h:50:19: note: Shift
bowtie2-2.5.4/bt2_idx.h:2757:11: style: Unused variable: name [unusedVariable]
bowtie2-2.5.4/unique.h:216:20: style: Variable 'secbest' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/unique.h:448:20: style: Variable 'secbest' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed_policy.cpp:41:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed_policy.cpp:326:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie2-2.5.4/ds.h:1770:4: error: Using 'memcpy' on class that contains a virtual function. [memsetClass]
bowtie2-2.5.4/ds.h:534:3: portability: Using memset() on class which contains a floating point number. [memsetClassFloat]
bowtie2-2.5.4/ds.h:541:3: portability: Using memset() on class which contains a floating point number. [memsetClassFloat]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::seq' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::qual' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::maxjump' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::seedoff' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::seedoffidx' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::seedtypeidx' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::fw' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:413:2: warning: Member variable 'InstantiatedSeed::nfiltered' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:615:2: warning: Member variable 'SeedResults::sorted_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:1648:2: warning: Member variable 'SeedAligner::ebwtFw_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:1648:2: warning: Member variable 'SeedAligner::ebwtBw_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:1648:2: warning: Member variable 'SeedAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:1648:2: warning: Member variable 'SeedAligner::read_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:1648:2: warning: Member variable 'SeedAligner::bwops_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.h:1648:2: warning: Member variable 'SeedAligner::bwedits_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_seed.cpp:1728:2: warning: Member variable 'SeedAlignerSearchState::lasttot' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/ds.h:1763:8: warning: Member variable 'ESet < SDnaStringExpandable < 1024 , 2 > >::cat_' is not assigned a value in 'ESet < SDnaStringExpandable < 1024 , 2 > >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < Seed , 128 >::cat_' is not assigned a value in 'EList < Seed , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < pair < int , int > , 128 >::cat_' is not assigned a value in 'EList < pair < int , int > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < InstantiatedSeed , 128 >::cat_' is not assigned a value in 'EList < InstantiatedSeed , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < QVal , 128 >::cat_' is not assigned a value in 'EList < QVal , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < SDnaStringExpandable < 1024 , 2 > , 128 >::cat_' is not assigned a value in 'EList < SDnaStringExpandable < 1024 , 2 > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < EEHit , 128 >::cat_' is not assigned a value in 'EList < EEHit , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < EList < InstantiatedSeed , 128 > , 128 >::cat_' is not assigned a value in 'EList < EList < InstantiatedSeed , 128 > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/aligner_seed.h:472:7: performance:inconclusive: Technically the member function 'InstantiatedSeed::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_seed.h:1655:7: performance:inconclusive: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_seed.cpp:472:14: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/aligner_seed.h:1655:7: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/aligner_seed.h:1815:7: style:inconclusive: Technically the member function 'SeedAligner::prefetchNextLocsBi' can be const. [functionConst]
bowtie2-2.5.4/aligner_seed.cpp:1326:14: note: Technically the member function 'SeedAligner::prefetchNextLocsBi' can be const.
bowtie2-2.5.4/aligner_seed.h:1815:7: note: Technically the member function 'SeedAligner::prefetchNextLocsBi' can be const.
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Seed , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Seed , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < pair < int , int > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < pair < int , int > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < InstantiatedSeed , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < InstantiatedSeed , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < QVal , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < QVal , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SDnaStringExpandable < 1024 , 2 > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SDnaStringExpandable < 1024 , 2 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < EEHit , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < EEHit , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < EList < InstantiatedSeed , 128 > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < EList < InstantiatedSeed , 128 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:1202:29: performance:inconclusive: Technically the member function 'ELList < uint32_t , 128 , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:1716:2: style: Class 'ESet < SDnaStringExpandable < 1024 , 2 > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/ds.h:1733:2: style: Class 'ESet < SDnaStringExpandable < 1024 , 2 > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_seed.h:1207:8: performance: Function 'exactFwEEHit()' should return member 'exactFwHit_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_seed.h:1212:8: performance: Function 'exactRcEEHit()' should return member 'exactRcHit_' by const reference. [returnByReference]
bowtie2-2.5.4/aligner_seed.cpp:1297:10: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_seed.cpp:1292:10: note: Assuming that condition 'ebwtfw' is not redundant
bowtie2-2.5.4/aligner_seed.cpp:1297:10: note: Condition 'ebwtfw' is always true
bowtie2-2.5.4/aligner_seed.cpp:1298:10: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_seed.cpp:1292:10: note: Assuming that condition 'ebwtfw' is not redundant
bowtie2-2.5.4/aligner_seed.cpp:1298:10: note: Condition 'ebwtfw' is always true
bowtie2-2.5.4/aligner_seed.cpp:1305:10: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_seed.cpp:1292:10: note: Assuming that condition 'ebwtfw' is not redundant
bowtie2-2.5.4/aligner_seed.cpp:1305:10: note: Condition 'ebwtfw' is always true
bowtie2-2.5.4/aligner_seed.cpp:1306:10: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_seed.cpp:1292:10: note: Assuming that condition 'ebwtfw' is not redundant
bowtie2-2.5.4/aligner_seed.cpp:1306:10: note: Condition 'ebwtfw' is always true
bowtie2-2.5.4/aligner_seed.cpp:1007:9: style: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'. [duplicateAssignExpression]
bowtie2-2.5.4/aligner_seed.cpp:1008:9: note: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'.
bowtie2-2.5.4/aligner_seed.cpp:1007:9: note: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'.
bowtie2-2.5.4/aligner_seed.cpp:333:15: style: The scope of the variable 'cons' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_seed.cpp:335:7: style: The scope of the variable 'q' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_seed.cpp:653:21: style: The scope of the variable 'srcache' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_seed.cpp:1129:9: style: The scope of the variable 'quc' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_seed.cpp:51:59: style:inconclusive: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_seed.h:277:55: note: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'.
bowtie2-2.5.4/aligner_seed.cpp:51:59: note: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'.
bowtie2-2.5.4/aligner_seed.cpp:223:20: style:inconclusive: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_seed.h:382:21: note: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'.
bowtie2-2.5.4/aligner_seed.cpp:223:20: note: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'.
bowtie2-2.5.4/aligner_seed.cpp:604:15: style:inconclusive: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_seed.h:1692:16: note: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'.
bowtie2-2.5.4/aligner_seed.cpp:604:15: note: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'.
bowtie2-2.5.4/aligner_seed.h:544:7: style: Local variable 'ns' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed.h:529:6: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed.h:544:7: note: Shadow variable
bowtie2-2.5.4/aligner_seed.cpp:1468:13: style: Local variable 'tloc' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_seed.cpp:1456:12: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed.cpp:1468:13: note: Shadow variable
bowtie2-2.5.4/aligner_seed.cpp:1468:19: style: Local variable 'bloc' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_seed.cpp:1456:18: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed.cpp:1468:19: note: Shadow variable
bowtie2-2.5.4/aligner_seed.cpp:131:34: performance: Function parameter '_cv' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_seed.h:1502:11: style: Variable 'el' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_seed.cpp:482:43: style: Variable 'seedlen' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1178:27: style: Variable 'tm[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1180:27: style: Variable 'bm[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1183:30: style: Variable 'tmp[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1185:30: style: Variable 'bmp[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1224:16: style: Variable 'offstr' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1464:8: style: Variable 't[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1464:15: style: Variable 't[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1464:22: style: Variable 't[2]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1464:29: style: Variable 't[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1465:8: style: Variable 'b[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1465:15: style: Variable 'b[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1465:22: style: Variable 'b[2]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_seed.cpp:1465:29: style: Variable 'b[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw.h:381:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw.cpp:43:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw.cpp:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw.cpp:173:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw.cpp:303:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw.cpp:504:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw.cpp:743:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_nuc.h:209:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_nuc.h:246:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_seed2.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie2-2.5.4/aligner_seed2.h:1242:7: performance:inconclusive: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_seed2.cpp:872:15: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/aligner_seed2.h:1242:7: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/aligner_seed2.cpp:1690:36: style: The comparison 'nopts == 1' is always true. [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_seed2.cpp:1620:18: note: 'nopts' is assigned value '1' here.
bowtie2-2.5.4/aligner_seed2.cpp:1690:36: note: The comparison 'nopts == 1' is always true.
bowtie2-2.5.4/aligner_seed2.cpp:1338:9: style: The scope of the variable 'nobranchDepth' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_seed2.cpp:629:17: style: Local variable 'topf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1286:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:629:17: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:629:39: style: Local variable 'botf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1287:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:629:39: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:637:11: style: Local variable 'edit' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1183:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:637:11: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:685:19: style: Local variable 'topf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1286:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:685:19: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:685:41: style: Local variable 'botf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1287:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:685:41: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:701:13: style: Local variable 'edit' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1183:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:701:13: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:722:40: style: Local variable 'topf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1286:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:722:40: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:723:40: style: Local variable 'botf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1287:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:723:40: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:731:14: style: Local variable 'edit' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1183:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:731:14: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:766:18: style: Local variable 'topf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1286:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:766:18: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:766:40: style: Local variable 'botf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1287:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:766:40: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:782:12: style: Local variable 'edit' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1183:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:782:12: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:800:36: style: Local variable 'topf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1286:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:800:36: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:801:36: style: Local variable 'botf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1287:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:801:36: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:809:13: style: Local variable 'edit' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1183:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:809:13: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1140:8: style: Local variable 'l2r' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1237:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1140:8: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1147:14: style: Local variable 'topf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1286:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1147:14: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1147:20: style: Local variable 'botf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1287:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1147:20: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1349:13: style: Local variable 'topf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1286:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1349:13: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1349:27: style: Local variable 'botf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1287:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1349:27: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1646:11: style: Local variable 'nopts' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_seed2.cpp:1620:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1646:11: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1728:11: style: Local variable 'al5pf' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1236:9: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1728:11: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1728:27: style: Local variable 'al5pi' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_seed2.h:1235:9: note: Shadowed declaration
bowtie2-2.5.4/aligner_seed2.cpp:1728:27: note: Shadow variable
bowtie2-2.5.4/aligner_seed2.cpp:1324:23: style: Parameter 'heap' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_seed2.cpp:1704:15: style: Variable 'tf' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/aligner_seed2.cpp:1705:15: style: Variable 'bf' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/aligner_seed2.cpp:1706:15: style: Variable 'tb' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/aligner_seed2.cpp:1707:15: style: Variable 'bb' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rd_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qu_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdfw_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdrc_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qufw_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qurc_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdi_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdf_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::fw_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::refidx_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::reflen_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rect_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rf_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rfi_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rff_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdgap_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rfgap_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::enable8_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::extend_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::minsc_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nceil_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sse8succ_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sse16succ_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseU8fwBuilt_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseU8rcBuilt_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseI16fwBuilt_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseI16rcBuilt_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltst_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltsc_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltdo_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DpNucFrame , 128 >::cat_' is not assigned a value in 'EList < DpNucFrame , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DpBtCandidate , 128 >::cat_' is not assigned a value in 'EList < DpBtCandidate , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/aligner_sw_nuc.h:119:14: style:inconclusive: Technically the member function 'DpBtCandidate::dominatedBy' can be const. [functionConst]
bowtie2-2.5.4/aligner_sw.h:342:7: style:inconclusive: Technically the member function 'SwAligner::printResultStacked' can be const. [functionConst]
bowtie2-2.5.4/aligner_sw.h:399:7: style:inconclusive: Technically the member function 'SwAligner::merge' can be const. [functionConst]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DpNucFrame , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DpNucFrame , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DpBtCandidate , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DpBtCandidate , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_seed2.cpp:1650:27: style: Variable 'nopts' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw.cpp:217:8: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_sw.cpp:354:8: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/pe.h:118:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pe.h:159:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ival_list.h:62:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ival_list.h:94:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ival_list.h:147:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ival_list.h:182:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ival_list.h:234:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ival_list.h:270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.h:198:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.h:224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.h:248:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.cpp:78:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.cpp:366:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.cpp:538:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.cpp:797:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.cpp:1441:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw.h:569:10: style: The scope of the variable 'nrej' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw.cpp:91:2: style: Unsigned expression 'readGaps' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_sw.cpp:92:2: style: Unsigned expression 'refGaps' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_sw.cpp:949:18: style: Local variable 'col' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw.cpp:769:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw.cpp:949:18: note: Shadow variable
bowtie2-2.5.4/aligner_sw.cpp:950:18: style: Local variable 'row' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw.cpp:768:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw.cpp:950:18: note: Shadow variable
bowtie2-2.5.4/aligner_sw_nuc.h:54:12: performance: Function parameter 'score_' should be passed by const reference. [passedByValue]
bowtie2-2.5.4/aligner_sw.cpp:624:12: style: Variable 'd8' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_sw.cpp:625:12: style: Variable 'd16' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_sw.cpp:773:13: style: Variable 'd' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_sw.cpp:782:13: style: Variable 'd' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_swsse.cpp:44:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.cpp:68:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.cpp:80:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse.cpp:48:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/aligner_swsse.cpp:88:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse.cpp:91:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse.cpp:43:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:203:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:295:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:781:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1207:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1317:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:192:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:296:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:776:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1182:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1292:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:772:5: style: The if condition is the same as the previous if condition [duplicateCondition]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:766:5: note: First condition
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:772:5: note: Second condition
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:594:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:647:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:648:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:649:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:697:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:698:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:699:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1121:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1217:29: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1376:25: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1384:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1389:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1435:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1436:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1437:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1492:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1493:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1494:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1495:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1496:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1497:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:677:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:678:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:677:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:372:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:356:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:372:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:378:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:357:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:378:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:383:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:358:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:383:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:389:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:359:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:389:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:392:2: style: Redundant initialization for 'vlo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:360:19: note: vlo is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:392:2: note: vlo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:404:2: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:361:19: note: vhilsw is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:404:2: note: vhilsw is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:401:2: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:362:19: note: vlolsw is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:401:2: note: vlolsw is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:397:2: style: Redundant initialization for 'vhi'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:396:19: note: vhi is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:397:2: note: vhi is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:835:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:814:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:835:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:841:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:815:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:841:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:846:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:816:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:846:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:852:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:817:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:852:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:855:2: style: Redundant initialization for 'vlo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:818:19: note: vlo is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:855:2: note: vlo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:867:2: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:819:19: note: vhilsw is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:867:2: note: vhilsw is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:864:2: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:820:19: note: vlolsw is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:864:2: note: vlolsw is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:860:2: style: Redundant initialization for 'vhi'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:859:19: note: vhi is initialized
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:860:2: note: vhi is overwritten
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:184:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:185:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:186:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:187:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:412:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:875:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1777:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1315:17: style:inconclusive: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw.h:546:18: note: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1315:17: note: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:76:8: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:76:8: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:592:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:368:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:592:12: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:631:10: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:631:10: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:635:17: style: Local variable 'j' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:478:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:635:17: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:695:16: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:448:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:695:16: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:152:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:184:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:185:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:186:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:187:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:417:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:418:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:419:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:767:5: style: The if condition is the same as the previous if condition [duplicateCondition]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:761:5: note: First condition
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:767:5: note: Second condition
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:583:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:636:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:637:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:638:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:689:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:691:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1096:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1192:29: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1354:25: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1362:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1367:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1413:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1414:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1415:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1470:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1471:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1472:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1473:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1474:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1475:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:669:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:670:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:669:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:373:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:357:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:373:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:379:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:358:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:379:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:384:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:359:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:384:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:390:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:360:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:390:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:399:2: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:369:19: note: vhilsw is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:399:2: note: vhilsw is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:831:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:809:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:831:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:837:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:810:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:837:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:842:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:811:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:842:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:848:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:812:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:848:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:854:2: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:824:19: note: vhilsw is initialized
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:854:2: note: vhilsw is overwritten
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:181:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:182:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:183:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:184:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:407:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:862:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1757:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1290:17: style:inconclusive: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw.h:537:18: note: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1290:17: note: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:76:8: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:76:8: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:581:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:367:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:581:12: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:620:10: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:620:10: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:624:17: style: Local variable 'j' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:471:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:624:17: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:687:16: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:443:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:687:16: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:149:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:181:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:182:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:183:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:184:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:412:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:413:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:414:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie2-2.5.4/aligner_sw_driver.cpp:1190:24: warning: Assert statement calls a function which may have desired side effects: 'matchesRef'. [assertWithSideEffect]
bowtie2-2.5.4/aligner_sw_driver.cpp:1234:25: warning: Assert statement calls a function which may have desired side effects: 'matchesRef'. [assertWithSideEffect]
bowtie2-2.5.4/aligner_sw_driver.cpp:1888:24: warning: Assert statement calls a function which may have desired side effects: 'matchesRef'. [assertWithSideEffect]
bowtie2-2.5.4/aligner_sw_driver.cpp:2102:45: warning: Assert statement calls a function which may have desired side effects: 'matchesRef'. [assertWithSideEffect]
bowtie2-2.5.4/aligner_sw_driver.cpp:2276:28: warning: Assert statement calls a function which may have desired side effects: 'matchesRef'. [assertWithSideEffect]
bowtie2-2.5.4/aligner_sw_driver.cpp:2321:26: warning: Assert statement calls a function which may have desired side effects: 'matchesRef'. [assertWithSideEffect]
bowtie2-2.5.4/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < PListSlice < uint32_t , 16384 > >::len' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:102:2: warning: Member variable 'SARangeWithOffs < PListSlice < uint32_t , 16384 > >::topf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:102:2: warning: Member variable 'SARangeWithOffs < PListSlice < uint32_t , 16384 > >::len' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < Interval , 128 >::cat_' is not assigned a value in 'EList < Interval , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < Coord , 128 >::cat_' is not assigned a value in 'EList < Coord , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < EIvalMergeList , 128 >::cat_' is not assigned a value in 'EList < EIvalMergeList , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < SATupleAndPos , 16 >::cat_' is not assigned a value in 'EList < SATupleAndPos , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < double , 128 >::cat_' is not assigned a value in 'EList < double , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < Random1toN , 16 >::cat_' is not assigned a value in 'EList < Random1toN , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < EEHit , 16 >::cat_' is not assigned a value in 'EList < EEHit , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < SATuple , 16 >::cat_' is not assigned a value in 'EList < SATuple , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < GroupWalk2S < PListSlice < uint32_t , 16384 > , 16 > , 128 >::cat_' is not assigned a value in 'EList < GroupWalk2S < PListSlice < uint32_t , 16384 > , 16 > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < ExtendRange , 128 >::cat_' is not assigned a value in 'EList < ExtendRange , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < GWState < PListSlice < uint32_t , 16384 > > , 16 >::cat_' is not assigned a value in 'EList < GWState < PListSlice < uint32_t , 16384 > > , 16 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/aligner_sw_driver.h:232:9: style:inconclusive: Technically the member function 'RowSampler::next' can be const. [functionConst]
bowtie2-2.5.4/group_walk.h:1150:7: style:inconclusive: Technically the member function 'GroupWalk2S < PListSlice < uint32_t , 16384 > , 16 >::resolveAll' can be const. [functionConst]
bowtie2-2.5.4/group_walk.h:385:7: performance:inconclusive: Technically the member function 'GWHit < PListSlice < uint32_t , 16384 > >::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Interval , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Interval , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Coord , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Coord , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < EIvalMergeList , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < EIvalMergeList , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SATupleAndPos , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SATupleAndPos , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < double , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < double , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Random1toN , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < Random1toN , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < EEHit , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < EEHit , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SATuple , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SATuple , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < GroupWalk2S < PListSlice < uint32_t , 16384 > , 16 > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < GroupWalk2S < PListSlice < uint32_t , 16384 > , 16 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < ExtendRange , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < ExtendRange , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < GWState < PListSlice < uint32_t , 16384 > > , 16 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < GWState < PListSlice < uint32_t , 16384 > > , 16 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aligner_sw_driver.h:183:2: style: Class 'RowSampler' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_sw_driver.h:300:2: style: Class 'SwDriver' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:203:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:295:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:939:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1427:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1624:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.cpp:519:37: style: Condition 'keepWhole' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_sw_driver.cpp:518:19: note: Assignment 'keepWhole=false', assigned value is 0
bowtie2-2.5.4/aligner_sw_driver.cpp:519:37: note: Condition 'keepWhole' is always false
bowtie2-2.5.4/aligner_sw_driver.cpp:792:13: warning: Either the condition 'msink!=NULL' is redundant or there is possible null pointer dereference: msink. [nullPointerRedundantCheck]
bowtie2-2.5.4/aligner_sw_driver.cpp:794:37: note: Assuming that condition 'msink!=NULL' is not redundant
bowtie2-2.5.4/aligner_sw_driver.cpp:792:13: note: Null pointer dereference
bowtie2-2.5.4/aligner_sw_driver.cpp:1947:8: style: Variable 'ominsc_cur' is assigned an expression that holds the same value. [redundantAssignment]
bowtie2-2.5.4/aligner_sw_driver.cpp:1940:27: note: ominsc_cur is assigned 'ominsc' here.
bowtie2-2.5.4/aligner_sw_driver.cpp:1947:8: note: Variable 'ominsc_cur' is assigned an expression that holds the same value.
bowtie2-2.5.4/aligner_sw_driver.cpp:637:9: style: The scope of the variable 'nlarge_elts' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:1102:12: style: The scope of the variable 'nsInLeftShift' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:1797:12: style: The scope of the variable 'nsInLeftShift' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:1925:11: style: The scope of the variable 'foundMate' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:2140:8: style: The scope of the variable 'refid' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:2141:16: style: The scope of the variable 'off1' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:2141:22: style: The scope of the variable 'off2' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:2142:15: style: The scope of the variable 'len1' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:2142:21: style: The scope of the variable 'len2' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:2143:13: style: The scope of the variable 'fw1' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:2143:18: style: The scope of the variable 'fw2' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_sw_driver.cpp:75:12: style:inconclusive: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw_driver.h:454:16: note: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'.
bowtie2-2.5.4/aligner_sw_driver.cpp:75:12: note: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'.
bowtie2-2.5.4/aligner_sw_driver.cpp:491:14: style:inconclusive: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw_driver.h:473:15: note: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'.
bowtie2-2.5.4/aligner_sw_driver.cpp:491:14: note: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'.
bowtie2-2.5.4/aligner_sw_driver.cpp:788:15: style:inconclusive: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw_driver.h:354:16: note: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'.
bowtie2-2.5.4/aligner_sw_driver.cpp:788:15: note: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'.
bowtie2-2.5.4/aligner_sw_driver.cpp:1395:13: style:inconclusive: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw_driver.h:379:14: note: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'.
bowtie2-2.5.4/aligner_sw_driver.cpp:1395:13: note: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'.
bowtie2-2.5.4/aligner_sw_driver.cpp:1422:23: style:inconclusive: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw_driver.h:406:24: note: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'.
bowtie2-2.5.4/aligner_sw_driver.cpp:1422:23: note: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'.
bowtie2-2.5.4/aligner_sw_driver.cpp:128:32: style: Local variable 'rn' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:106:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:128:32: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:150:32: style: Local variable 'width' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:122:28: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:150:32: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:166:36: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:148:25: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:166:36: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:239:21: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:206:14: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:239:21: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:241:28: style: Local variable 'width' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:213:24: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:241:28: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:256:28: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:239:21: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:256:28: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:348:13: style: Local variable 'tloc' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:316:12: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:348:13: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:348:19: style: Local variable 'bloc' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:316:18: note: Shadowed declaration
bowtie2-2.5.4/aligner_sw_driver.cpp:348:19: note: Shadow variable
bowtie2-2.5.4/aligner_sw_driver.cpp:534:25: style: Variable 'range' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/aligner_sw_driver.cpp:757:8: style: Parameter 'rd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_sw_driver.cpp:790:8: style: Parameter 'exhaustive' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:217:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:307:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:928:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1396:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1597:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_sw_driver.cpp:344:8: style: Variable 't[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:344:15: style: Variable 't[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:344:22: style: Variable 't[2]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:344:29: style: Variable 't[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:345:8: style: Variable 'b[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:345:15: style: Variable 'b[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:345:22: style: Variable 'b[2]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:345:29: style: Variable 'b[3]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:641:16: style: Variable 'nlarge_elts' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:643:16: style: Variable 'nlarge_elts' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_sw_driver.cpp:1925:21: style: Variable 'foundMate' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:930:5: style: The if condition is the same as the previous if condition [duplicateCondition]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:924:5: note: First condition
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:930:5: note: Second condition
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:685:33: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:687:12: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:737:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:738:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:739:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:787:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:789:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:868:32: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:870:11: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1460:32: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1461:33: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1499:33: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1688:25: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1696:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1701:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1751:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1752:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1753:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1808:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1809:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1810:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1811:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1812:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1813:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:767:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:768:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:767:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:376:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:358:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:376:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:382:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:359:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:382:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:387:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:360:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:387:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:393:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:361:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:393:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:396:2: style: Redundant initialization for 'vlo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:362:19: note: vlo is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:396:2: note: vlo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:408:2: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:363:19: note: vlolsw is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:408:2: note: vlolsw is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:405:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:364:19: note: vmax is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:405:7: note: vmax is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:401:2: style: Redundant initialization for 'vhi'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:400:19: note: vhi is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:401:2: note: vhi is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:985:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:970:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:985:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:991:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:971:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:991:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:996:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:972:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:996:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1002:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:973:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1002:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1005:2: style: Redundant initialization for 'vlo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:974:19: note: vlo is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1005:2: note: vlo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1017:2: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:975:19: note: vlolsw is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1017:2: note: vlolsw is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1014:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:976:19: note: vmax is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1014:7: note: vmax is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1010:2: style: Redundant initialization for 'vhi'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1009:19: note: vhi is initialized
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1010:2: note: vhi is overwritten
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:184:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:185:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:186:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:187:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1025:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:2098:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1439:49: warning: Either the condition '(bonus)>(0)' is redundant or there is division by zero at line 1439. [zerodivcond]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1438:2: note: Assuming that condition '(bonus)>(0)' is not redundant
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1439:49: note: Division by zero
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1622:17: style:inconclusive: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw.h:528:18: note: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1622:17: note: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:76:8: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:76:8: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:676:9: style: Local variable 'cmp' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:616:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:676:9: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:721:10: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:721:10: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:725:17: style: Local variable 'j' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:545:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:725:17: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:785:16: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:453:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:785:16: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:152:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:184:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:185:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:186:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:187:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:421:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:423:20: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:424:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aln_sink.cpp:74:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:108:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:157:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:222:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:313:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:334:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:361:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:699:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:1505:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.cpp:1649:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:919:5: style: The if condition is the same as the previous if condition [duplicateCondition]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:912:5: note: First condition
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:919:5: note: Second condition
bowtie2-2.5.4/banded.h:33:7: performance:inconclusive: Technically the member function 'BandedSseAligner::init' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/banded.h:44:7: performance:inconclusive: Technically the member function 'BandedSseAligner::nextAlignment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/banded.h:34:11: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/banded.h:37:11: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:683:11: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:684:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:734:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:735:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:736:24: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:783:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:785:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:866:10: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:867:21: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1426:31: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1463:32: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1656:25: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1664:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1669:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1715:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1716:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1717:26: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1772:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1773:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1774:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1775:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1776:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1777:41: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:763:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:764:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:763:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:391:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:371:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:391:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:397:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:372:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:397:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:402:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:373:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:402:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:408:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:374:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:408:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:416:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:377:19: note: vmax is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:416:7: note: vmax is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:419:2: style: Redundant initialization for 'vbias'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:386:19: note: vbias is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:419:2: note: vbias is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:412:2: style: Redundant initialization for 'vbiasm1'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:387:19: note: vbiasm1 is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:412:2: note: vbiasm1 is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:977:2: style: Redundant initialization for 'rfgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:960:19: note: rfgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:977:2: note: rfgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:983:2: style: Redundant initialization for 'rfgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:961:19: note: rfgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:983:2: note: rfgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:988:2: style: Redundant initialization for 'rdgapo'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:962:19: note: rdgapo is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:988:2: note: rdgapo is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:994:2: style: Redundant initialization for 'rdgape'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:963:19: note: rdgape is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:994:2: note: rdgape is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:998:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:966:19: note: vmax is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:998:7: note: vmax is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1001:2: style: Redundant initialization for 'vbias'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:973:19: note: vbias is initialized
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1001:2: note: vbias is overwritten
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:198:12: style: The scope of the variable 'sc_h_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:199:12: style: The scope of the variable 'sc_e_left' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:200:12: style: The scope of the variable 'sc_h_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:201:12: style: The scope of the variable 'sc_f_up' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1009:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:2055:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1408:49: warning: Either the condition '(bonus)>(0)' is redundant or there is division by zero at line 1408. [zerodivcond]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1407:2: note: Assuming that condition '(bonus)>(0)' is not redundant
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1408:49: note: Division by zero
bowtie2-2.5.4/bowtie_build_main.cpp:63:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1595:17: style:inconclusive: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
bowtie2-2.5.4/aligner_sw.h:519:18: note: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1595:17: note: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:76:8: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:76:8: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:674:9: style: Local variable 'cmp' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:615:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:674:9: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:718:10: style: Local variable 'done' shadows outer function [shadowFunction]
bowtie2-2.5.4/aligner_sw.h:354:7: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:718:10: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:722:17: style: Local variable 'j' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:542:10: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:722:17: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:781:16: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:461:13: note: Shadowed declaration
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:781:16: note: Shadow variable
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:166:11: style: Parameter 'd' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/bowtie_build_main.cpp:54:27: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:198:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:199:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:200:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:201:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:432:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:433:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:434:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bowtie_main.cpp:62:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bowtie_main.cpp:53:27: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_build.cpp:125:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BOWTIE2_VERSION [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_build.cpp:252:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_build.cpp:356:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_build.cpp:366:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_build.cpp:386:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_build.cpp:223:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_dp.cpp:139:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_dp.cpp:192:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_dp.cpp:233:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_dp.cpp:290:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_dp.cpp:487:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_dp.cpp:567:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_dp.cpp:648:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable opterr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aln_sink.h:762:7: performance:inconclusive: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/aln_sink.cpp:349:15: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/aln_sink.h:762:7: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/aln_sink.h:1357:7: style:inconclusive: Technically the member function 'AlnSinkSam::appendMate' can be const. [functionConst]
bowtie2-2.5.4/aln_sink.cpp:1889:18: note: Technically the member function 'AlnSinkSam::appendMate' can be const.
bowtie2-2.5.4/aln_sink.h:1357:7: note: Technically the member function 'AlnSinkSam::appendMate' can be const.
bowtie2-2.5.4/aln_sink.cpp:548:39: style: Condition 'rd1_==NULL' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aln_sink.cpp:548:23: note: Assuming that condition 'rd1==NULL' is not redundant
bowtie2-2.5.4/aln_sink.cpp:545:21: note: Assuming that condition '(rd1_==NULL)==(rd1==NULL)' is not redundant
bowtie2-2.5.4/aln_sink.cpp:548:39: note: Condition 'rd1_==NULL' is always true
bowtie2-2.5.4/aln_sink.cpp:419:12: style: The scope of the variable 'ncondiscord_0' can be reduced. [variableScope]
bowtie2-2.5.4/aln_sink.cpp:1902:14: style:inconclusive: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'. [funcArgNamesDifferent]
bowtie2-2.5.4/aln_sink.h:1370:15: note: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'.
bowtie2-2.5.4/aln_sink.cpp:1902:14: note: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'.
bowtie2-2.5.4/aln_sink.cpp:1896:10: style: Parameter 'rso' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/bt2_build.cpp:604:13: style: Condition 'optind>=argc' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/bt2_build.cpp:596:13: note: Assuming that condition 'optind>=argc' is not redundant
bowtie2-2.5.4/bt2_build.cpp:604:13: note: Condition 'optind>=argc' is always false
bowtie2-2.5.4/bt2_build.cpp:671:7: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_build.cpp:690:6: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_build.cpp:235:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bowtie2-2.5.4/bt2_build.cpp:666:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_build.cpp:685:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < DpProblem , 128 >::cat_' is not assigned a value in 'EList < DpProblem , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < DpProblem , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < DpProblem , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/bt2_dp.cpp:452:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
bowtie2-2.5.4/bt2_dp.cpp:201:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bowtie2-2.5.4/bt2_dp.cpp:482:6: style: The scope of the variable 'next_option' can be reduced. [variableScope]
bowtie2-2.5.4/bt2_dp.cpp:616:15: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_dp.cpp:570:14: note: Shadowed declaration
bowtie2-2.5.4/bt2_dp.cpp:616:15: note: Shadow variable
bowtie2-2.5.4/bt2_idx.cpp:71:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.cpp:132:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.cpp:152:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.cpp:184:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.cpp:231:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.cpp:280:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_locks.cpp:6:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_locks.cpp:16:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_locks.cpp:30:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_locks.cpp:35:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_io.cpp:56:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_io.cpp:644:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_io.cpp:732:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_io.cpp:743:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_io.cpp:837:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_io.cpp:884:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_io.cpp:938:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_idx.cpp:80:14: style: The scope of the variable 'fraglen' can be reduced. [variableScope]
bowtie2-2.5.4/bt2_idx.cpp:202:14: style:inconclusive: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'. [funcArgNamesDifferent]
bowtie2-2.5.4/bt2_idx.h:1277:15: note: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'.
bowtie2-2.5.4/bt2_idx.cpp:202:14: note: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'.
bowtie2-2.5.4/bt2_idx.cpp:203:14: style:inconclusive: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'. [funcArgNamesDifferent]
bowtie2-2.5.4/bt2_idx.h:1278:15: note: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'.
bowtie2-2.5.4/bt2_idx.cpp:203:14: note: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'.
bowtie2-2.5.4/bt2_io.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie2-2.5.4/bt2_io.cpp:717:9: warning: Assert statement calls a function which may have desired side effects: 'ferror'. [assertWithSideEffect]
bowtie2-2.5.4/concurrentqueue.h:3243:63: debug: Failed to instantiate template "create". The checking continues anyway. [templateInstantiation]
bowtie2-2.5.4/concurrentqueue.h:1018:10: debug: Failed to instantiate template "inner_enqueue". The checking continues anyway. [templateInstantiation]
bowtie2-2.5.4/concurrentqueue.h:998:15: debug: Failed to instantiate template "inner_enqueue". The checking continues anyway. [templateInstantiation]
bowtie2-2.5.4/bt2_io.cpp:177:18: style: Redundant condition: The condition 'color != -1' is redundant since '!color' is sufficient. [redundantCondition]
bowtie2-2.5.4/bt2_io.cpp:443:8: style: Condition 'loadFtab' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/bt2_io.cpp:421:6: note: Assuming that condition 'loadFtab' is not redundant
bowtie2-2.5.4/bt2_io.cpp:443:8: note: Condition 'loadFtab' is always true
bowtie2-2.5.4/bt2_io.cpp:272:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/concurrentqueue.h:1671:3: debug: Failed to instantiate template "identity". The checking continues anyway. [templateInstantiation]
bowtie2-2.5.4/bt2_io.cpp:263:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:310:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:360:18: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:363:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:434:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:464:17: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:499:7: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:558:18: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:566:29: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:586:20: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:589:19: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:847:15: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_io.cpp:700:5: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/bt2_io.cpp:696:10: note: c is initialized
bowtie2-2.5.4/bt2_io.cpp:700:5: note: c is overwritten
bowtie2-2.5.4/bt2_io.cpp:206:14: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1242:27: note: Shadowed declaration
bowtie2-2.5.4/bt2_io.cpp:206:14: note: Shadow variable
bowtie2-2.5.4/bt2_io.cpp:337:8: style: Local variable 'shmemLeader' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_io.cpp:276:7: note: Shadowed declaration
bowtie2-2.5.4/bt2_io.cpp:337:8: note: Shadow variable
bowtie2-2.5.4/bt2_io.cpp:586:13: style: Local variable 'offs' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1251:23: note: Shadowed declaration
bowtie2-2.5.4/bt2_io.cpp:586:13: note: Shadow variable
bowtie2-2.5.4/bt2_io.cpp:805:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1242:27: note: Shadowed declaration
bowtie2-2.5.4/bt2_io.cpp:805:20: note: Shadow variable
bowtie2-2.5.4/bt2_io.cpp:880:2: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1242:27: note: Shadowed declaration
bowtie2-2.5.4/bt2_io.cpp:880:2: note: Shadow variable
bowtie2-2.5.4/bt2_io.cpp:269:22: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_io.cpp:351:23: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_io.cpp:488:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_io.cpp:528:24: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/bt2_util.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_util.cpp:87:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_util.cpp:151:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_util.cpp:203:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1625:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable I [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1779:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1823:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1839:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1851:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1931:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1940:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1997:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:2087:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:156:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/diff_sample.h:706:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:1619:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1630:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1655:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1667:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1679:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::cs_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::printcs_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::zero_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning:inconclusive: Member variable 'SStringExpandable::zeroT_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::len_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::sz_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
bowtie2-2.5.4/ls.h:43:1: style: The class 'LarssonSadakane' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
bowtie2-2.5.4/sstring.h:1861:7: style:inconclusive: Technically the member function 'SStringExpandable::operator==' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1868:7: style:inconclusive: Technically the member function 'SStringExpandable::operator!=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1875:7: style:inconclusive: Technically the member function 'SStringExpandable::operator<' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1882:7: style:inconclusive: Technically the member function 'SStringExpandable::operator>' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1889:7: style:inconclusive: Technically the member function 'SStringExpandable::operator<=' can be const. [functionConst]
bowtie2-2.5.4/sstring.h:1896:7: style:inconclusive: Technically the member function 'SStringExpandable::operator>=' can be const. [functionConst]
bowtie2-2.5.4/ls.h:187:14: performance:inconclusive: Technically the member function 'LarssonSadakane::bucketsort' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/filebuf.h:565:3: warning: Class 'BitpairOutFileBuf' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie2-2.5.4/filebuf.h:565:3: warning: Class 'BitpairOutFileBuf' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/filebuf.h:565:3: warning: Class 'BitpairOutFileBuf' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
bowtie2-2.5.4/filebuf.h:658:3: warning: Class 'OutFileBuf' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie2-2.5.4/filebuf.h:658:3: warning: Class 'OutFileBuf' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const std::basic_string<T>&str)' at line 1661. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1661:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const T*b,long sz)' at line 1673. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1673:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:1822:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const T*b)' at line 1685. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:1685:3: note: Calling install
bowtie2-2.5.4/sstring.h:1822:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:3008:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2846. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2846:5: note: Calling installColors
bowtie2-2.5.4/sstring.h:3008:15: note: installColors is a virtual function
bowtie2-2.5.4/sstring.h:3000:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2848. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2848:5: note: Calling installChars
bowtie2-2.5.4/sstring.h:3000:15: note: installChars is a virtual function
bowtie2-2.5.4/sstring.h:2986:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2867. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2867:5: note: Calling installColors
bowtie2-2.5.4/sstring.h:2986:15: note: installColors is a virtual function
bowtie2-2.5.4/sstring.h:2972:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2869. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2869:5: note: Calling installChars
bowtie2-2.5.4/sstring.h:2972:15: note: installChars is a virtual function
bowtie2-2.5.4/sstring.h:2957:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2872. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2872:4: note: Calling install
bowtie2-2.5.4/sstring.h:2957:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:2938:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const char*b,bool chars=false,bool colors=false)' at line 2885. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2885:3: note: Calling install
bowtie2-2.5.4/sstring.h:2938:15: note: install is a virtual function
bowtie2-2.5.4/sstring.h:3015:7: warning: The class 'SDnaStringExpandable' defines member function with name 'set' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1770:7: note: Parent function 'SStringExpandable::set'
bowtie2-2.5.4/sstring.h:3015:7: note: Derived function 'SDnaStringExpandable::set'
bowtie2-2.5.4/sstring.h:3063:21: warning: The class 'SDnaStringExpandable' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1798:11: note: Parent function 'SStringExpandable::operator[]'
bowtie2-2.5.4/sstring.h:3063:21: note: Derived function 'SDnaStringExpandable::operator[]'
bowtie2-2.5.4/sstring.h:3070:21: warning: The class 'SDnaStringExpandable' defines member function with name 'get' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1814:11: note: Parent function 'SStringExpandable::get'
bowtie2-2.5.4/sstring.h:3070:21: note: Derived function 'SDnaStringExpandable::get'
bowtie2-2.5.4/sstring.h:3253:7: warning: The class 'SDnaMaskString' defines member function with name 'set' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1770:7: note: Parent function 'SStringExpandable::set'
bowtie2-2.5.4/sstring.h:3253:7: note: Derived function 'SDnaMaskString::set'
bowtie2-2.5.4/sstring.h:3301:14: warning: The class 'SDnaMaskString' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1798:11: note: Parent function 'SStringExpandable::operator[]'
bowtie2-2.5.4/sstring.h:3301:14: note: Derived function 'SDnaMaskString::operator[]'
bowtie2-2.5.4/sstring.h:3308:8: warning: The class 'SDnaMaskString' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1806:5: note: Parent function 'SStringExpandable::operator[]'
bowtie2-2.5.4/sstring.h:3308:8: note: Derived function 'SDnaMaskString::operator[]'
bowtie2-2.5.4/sstring.h:3315:14: warning: The class 'SDnaMaskString' defines member function with name 'get' also defined in its parent class 'SStringExpandable'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1814:11: note: Parent function 'SStringExpandable::get'
bowtie2-2.5.4/sstring.h:3315:14: note: Derived function 'SDnaMaskString::get'
bowtie2-2.5.4/diff_sample.h:703:2: style: Class 'VSorting_worker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/sstring.h:2888:11: style: The destructor '~SDnaStringExpandable' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/sstring.h:1691:11: note: Virtual destructor in base class
bowtie2-2.5.4/sstring.h:2888:11: note: Destructor in derived class
bowtie2-2.5.4/sstring.h:3160:11: style: The destructor '~SDnaMaskString' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/sstring.h:1691:11: note: Virtual destructor in base class
bowtie2-2.5.4/sstring.h:3160:11: note: Destructor in derived class
bowtie2-2.5.4/diff_sample.h:707:33: style: Variable 'dcs' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/ls.h:127:38: style: Variable 'pn' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/diff_sample.h:827:8: style: Instance of 'VSorting_worker' object is destroyed immediately. [unusedScopedObject]
bowtie2-2.5.4/bt2_util.cpp:204:5: warning: Either the condition '-1!=(lastorig)' is redundant or the array 'dinuc2color[5][5]' is accessed at index dinuc2color[*][-1], which is out of bounds. [negativeIndex]
bowtie2-2.5.4/bt2_util.cpp:203:5: note: Assuming that condition '-1!=(lastorig)' is not redundant
bowtie2-2.5.4/bt2_util.cpp:204:5: note: Negative array index
bowtie2-2.5.4/dp_framer.cpp:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/dp_framer.cpp:191:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/dp_framer.cpp:305:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_util.cpp:186:7: style: Condition 'mirror' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/bt2_util.cpp:177:5: note: Assuming that condition 'mirror' is not redundant
bowtie2-2.5.4/bt2_util.cpp:186:7: note: Condition 'mirror' is always false
bowtie2-2.5.4/bt2_util.cpp:100:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
bowtie2-2.5.4/bt2_util.cpp:118:3: style: Unsigned expression 'this->plen()[i]' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/bitpack.h:39:17: error: Shifting by a negative value is undefined behaviour [shiftNegative]
bowtie2-2.5.4/bt2_util.cpp:44:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1242:27: note: Shadowed declaration
bowtie2-2.5.4/bt2_util.cpp:44:20: note: Shadow variable
bowtie2-2.5.4/bt2_util.cpp:45:7: style: Local variable 'fw' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1265:14: note: Shadowed declaration
bowtie2-2.5.4/bt2_util.cpp:45:7: note: Shadow variable
bowtie2-2.5.4/bt2_util.cpp:83:20: style: Local variable 'eh' shadows outer function [shadowFunction]
bowtie2-2.5.4/bt2_idx.h:1242:27: note: Shadowed declaration
bowtie2-2.5.4/bt2_util.cpp:83:20: note: Shadow variable
bowtie2-2.5.4/bt2_util.cpp:98:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/ds.cpp:44:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:66:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:129:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:206:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:302:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:378:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:416:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:441:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/edit.cpp:456:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/sstring.h:3015:7: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'set' also defined in its parent class 'SStringExpandable < char , 1024 , 2 , 0 >'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1770:7: note: Parent function 'SStringExpandable < char , 1024 , 2 , 0 >::set'
bowtie2-2.5.4/sstring.h:3015:7: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::set'
bowtie2-2.5.4/sstring.h:3024:7: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'append' also defined in its parent class 'SStringExpandable < char , 1024 , 2 , 0 >'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1778:7: note: Parent function 'SStringExpandable < char , 1024 , 2 , 0 >::append'
bowtie2-2.5.4/sstring.h:3024:7: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::append'
bowtie2-2.5.4/sstring.h:3063:21: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'operator[]' also defined in its parent class 'SStringExpandable < char , 1024 , 2 , 0 >'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1798:11: note: Parent function 'SStringExpandable < char , 1024 , 2 , 0 >::operator[]'
bowtie2-2.5.4/sstring.h:3063:21: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::operator[]'
bowtie2-2.5.4/sstring.h:3070:21: warning: The class 'SDnaStringExpandable < 1024 , 2 >' defines member function with name 'get' also defined in its parent class 'SStringExpandable < char , 1024 , 2 , 0 >'. [duplInheritedMember]
bowtie2-2.5.4/sstring.h:1814:11: note: Parent function 'SStringExpandable < char , 1024 , 2 , 0 >::get'
bowtie2-2.5.4/sstring.h:3070:21: note: Derived function 'SDnaStringExpandable < 1024 , 2 >::get'
bowtie2-2.5.4/sstring.h:2888:11: style: The destructor '~SDnaStringExpandable < 1024 , 2 >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/sstring.h:1691:11: note: Virtual destructor in base class
bowtie2-2.5.4/sstring.h:2888:11: note: Destructor in derived class
bowtie2-2.5.4/sstring.h:2957:15: style: The function 'install' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/sstring.h:1822:15: note: Virtual function in base class
bowtie2-2.5.4/sstring.h:2957:15: note: Function in derived class
bowtie2-2.5.4/sstring.h:3115:22: style: The function 'toZBuf' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/sstring.h:2048:19: note: Virtual function in base class
bowtie2-2.5.4/sstring.h:3115:22: note: Function in derived class
bowtie2-2.5.4/edit.cpp:367:9: style:inconclusive: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'. [funcArgNamesDifferent]
bowtie2-2.5.4/edit.h:301:10: note: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'.
bowtie2-2.5.4/edit.cpp:367:9: note: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'.
bowtie2-2.5.4/edit.cpp:368:9: style:inconclusive: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'. [funcArgNamesDifferent]
bowtie2-2.5.4/edit.h:302:10: note: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'.
bowtie2-2.5.4/edit.cpp:368:9: note: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'.
bowtie2-2.5.4/edit.cpp:438:32: style:inconclusive: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'. [funcArgNamesDifferent]
bowtie2-2.5.4/edit.h:226:34: note: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'.
bowtie2-2.5.4/edit.cpp:438:32: note: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'.
bowtie2-2.5.4/edit.cpp:455:32: style:inconclusive: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'. [funcArgNamesDifferent]
bowtie2-2.5.4/edit.h:231:34: note: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'.
bowtie2-2.5.4/edit.cpp:455:32: note: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'.
bowtie2-2.5.4/concurrentqueue.h:495:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:512:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:699:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3705:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3713:114: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:164:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:184:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:486:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:504:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:712:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.h:1092:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/aligner_metrics.h:138:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:274:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:690:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:719:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BOWTIE2_VERSION [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:925:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:985:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:1025:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:1612:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:2715:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:2800:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:2818:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:2836:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:2855:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:2913:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:3083:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4228:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4506:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4519:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4543:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4583:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4653:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4692:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:4820:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:820:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:844:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:861:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:922:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1132:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1170:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1191:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1234:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1251:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1328:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1342:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1369:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1376:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1382:115: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1389:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1395:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1453:138: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1466:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1478:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1513:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1526:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1572:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1599:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1618:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1639:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1654:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1739:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1744:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1796:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1851:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1957:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2060:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2250:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2362:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2446:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2489:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2554:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2587:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2637:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2782:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2903:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2937:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2954:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:2968:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3058:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3108:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3233:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3253:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3284:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3303:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3338:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3364:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3407:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3581:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3597:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3607:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3630:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:3637:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:1572:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable explicit_context [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:488:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/concurrentqueue.h:479:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:1264:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.h:1270:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/outq.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/outq.cpp:63:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/group_walk.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie2-2.5.4/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs::len' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:102:2: warning: Member variable 'SARangeWithOffs::topf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:102:2: warning: Member variable 'SARangeWithOffs::len' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/group_walk.h:385:7: performance:inconclusive: Technically the member function 'GWHit::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/group_walk.h:1150:7: style:inconclusive: Technically the member function 'GroupWalk2S::resolveAll' can be const. [functionConst]
bowtie2-2.5.4/outq.cpp:107:9: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/pe.cpp:46:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pe.cpp:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pe.cpp:181:2: style: Unsigned expression 'minfrag_' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/presets.cpp:93:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/endian_swap.h:118:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:59:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:108:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:163:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:213:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:253:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:330:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:458:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:502:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:614:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:652:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readOrigBuf [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:698:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:776:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:853:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:957:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readOrigBuf [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1004:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1052:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1138:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1263:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1550:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1680:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1711:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1719:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/pat.cpp:1725:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: pair < int , std :: string > , 128 >::cat_' is not assigned a value in 'EList < std :: pair < int , std :: string > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: pair < int , std :: string > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < std :: pair < int , std :: string > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/presets.h:57:11: style: The destructor '~PresetsV0' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/presets.h:39:11: note: Virtual destructor in base class
bowtie2-2.5.4/presets.h:57:11: note: Destructor in derived class
bowtie2-2.5.4/presets.h:59:15: style: The function 'apply' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/presets.h:41:15: note: Virtual function in base class
bowtie2-2.5.4/presets.h:59:15: note: Function in derived class
bowtie2-2.5.4/presets.h:64:23: style: The function 'name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/presets.h:46:23: note: Virtual function in base class
bowtie2-2.5.4/presets.h:64:23: note: Function in derived class
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::format' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::interleaved' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::fileParallel' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::seed' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::max_buf' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::solexa64' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::phred64' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::intQuals' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::trim5' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::trim3' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::sampleLen' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::sampleFreq' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::skip' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::upto' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::nthreads' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::fixName' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::preserve_tags' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:75:2: warning:inconclusive: Member variable 'PatternParams::align_paired_reads' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:700:2: warning: Member variable 'FastaContinuousPatternSource::buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/pat.h:700:2: warning: Member variable 'FastaContinuousPatternSource::name_int_buf_' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < Read , 128 >::cat_' is not assigned a value in 'EList < Read , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < SStringExpandable < char , 1024 , 2 , 1024 > , 128 >::cat_' is not assigned a value in 'EList < SStringExpandable < char , 1024 , 2 , 1024 > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < PatternSource * , 128 >::cat_' is not assigned a value in 'EList < PatternSource * , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < PatternSourcePerThread * , 128 >::cat_' is not assigned a value in 'EList < PatternSourcePerThread * , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/pat.h:492:7: performance:inconclusive: Technically the member function 'CFilePatternSource::is_gzipped_file' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/pat.h:1205:7: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalize' can be const. [functionConst]
bowtie2-2.5.4/pat.cpp:119:30: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
bowtie2-2.5.4/pat.h:1205:7: note: Technically the member function 'PatternSourcePerThread::finalize' can be const.
bowtie2-2.5.4/pat.h:1212:7: style:inconclusive: Technically the member function 'PatternSourcePerThread::finalizePair' can be const. [functionConst]
bowtie2-2.5.4/pat.cpp:134:30: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
bowtie2-2.5.4/pat.h:1212:7: note: Technically the member function 'PatternSourcePerThread::finalizePair' can be const.
bowtie2-2.5.4/pat.h:1222:7: style:inconclusive: Technically the member function 'PatternSourcePerThread::trim' can be const. [functionConst]
bowtie2-2.5.4/pat.h:1332:8: style:inconclusive: Technically the member function 'LockedQueue < PatternSourcePerThread * >::empty' can be const. [functionConst]
bowtie2-2.5.4/pat.h:1332:8: style:inconclusive: Technically the member function 'LockedQueue < ReadElement >::empty' can be const. [functionConst]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < Read , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < SStringExpandable < char , 1024 , 2 , 1024 > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < SStringExpandable < char , 1024 , 2 , 1024 > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < PatternSource * , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < PatternSourcePerThread * , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/concurrentqueue.h:1300:14: performance:inconclusive: Technically the member function 'ConcurrentQueue < PatternSourcePerThread * , ConcurrentQueueDefaultTraits >::try_dequeue_from_producer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/concurrentqueue.h:1313:16: performance:inconclusive: Technically the member function 'ConcurrentQueue < PatternSourcePerThread * , ConcurrentQueueDefaultTraits >::try_dequeue_bulk_from_producer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/concurrentqueue.h:1300:14: performance:inconclusive: Technically the member function 'ConcurrentQueue < ReadElement , ConcurrentQueueDefaultTraits >::try_dequeue_from_producer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/concurrentqueue.h:1313:16: performance:inconclusive: Technically the member function 'ConcurrentQueue < ReadElement , ConcurrentQueueDefaultTraits >::try_dequeue_bulk_from_producer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/pat.h:740:15: style: Virtual function 'resetForNextFile' is called from constructor 'FastaContinuousPatternSource(const EList < std :: string , 128 >&infiles,const PatternParams&p)' at line 713. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/pat.h:713:3: note: Calling resetForNextFile
bowtie2-2.5.4/pat.h:740:15: note: resetForNextFile is a virtual function
bowtie2-2.5.4/pat.h:610:7: warning: The class 'FastaPatternSource' defines member variable with name 'first_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie2-2.5.4/pat.h:542:7: note: Parent variable 'CFilePatternSource::first_'
bowtie2-2.5.4/pat.h:610:7: note: Derived variable 'FastaPatternSource::first_'
bowtie2-2.5.4/pat.h:756:7: warning: The class 'FastaContinuousPatternSource' defines member variable with name 'buf_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie2-2.5.4/pat.h:543:7: note: Parent variable 'CFilePatternSource::buf_'
bowtie2-2.5.4/pat.h:756:7: note: Derived variable 'FastaContinuousPatternSource::buf_'
bowtie2-2.5.4/pat.h:809:7: warning: The class 'FastqPatternSource' defines member variable with name 'first_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie2-2.5.4/pat.h:542:7: note: Parent variable 'CFilePatternSource::first_'
bowtie2-2.5.4/pat.h:809:7: note: Derived variable 'FastqPatternSource::first_'
bowtie2-2.5.4/pat.h:898:7: warning: The class 'BAMPatternSource' defines member variable with name 'first_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie2-2.5.4/pat.h:542:7: note: Parent variable 'CFilePatternSource::first_'
bowtie2-2.5.4/pat.h:898:7: note: Derived variable 'BAMPatternSource::first_'
bowtie2-2.5.4/pat.h:916:16: warning: The class 'BAMPatternSource' defines member variable with name 'pp_' also defined in its parent class 'PatternSource'. [duplInheritedMember]
bowtie2-2.5.4/pat.h:280:23: note: Parent variable 'PatternSource::pp_'
bowtie2-2.5.4/pat.h:916:16: note: Derived variable 'BAMPatternSource::pp_'
bowtie2-2.5.4/pat.h:962:7: warning: The class 'RawPatternSource' defines member variable with name 'first_' also defined in its parent class 'CFilePatternSource'. [duplInheritedMember]
bowtie2-2.5.4/pat.h:542:7: note: Parent variable 'CFilePatternSource::first_'
bowtie2-2.5.4/pat.h:962:7: note: Derived variable 'RawPatternSource::first_'
bowtie2-2.5.4/concurrentqueue.h:1955:8: warning: The struct 'ExplicitProducer' defines member function with name 'dequeue' also defined in its parent struct 'ProducerBase'. [duplInheritedMember]
bowtie2-2.5.4/concurrentqueue.h:1714:15: note: Parent function 'ProducerBase::dequeue'
bowtie2-2.5.4/concurrentqueue.h:1955:8: note: Derived function 'ExplicitProducer::dequeue'
bowtie2-2.5.4/concurrentqueue.h:2248:10: warning: The struct 'ExplicitProducer' defines member function with name 'dequeue_bulk' also defined in its parent struct 'ProducerBase'. [duplInheritedMember]
bowtie2-2.5.4/concurrentqueue.h:1725:17: note: Parent function 'ProducerBase::dequeue_bulk'
bowtie2-2.5.4/concurrentqueue.h:2248:10: note: Derived function 'ExplicitProducer::dequeue_bulk'
bowtie2-2.5.4/concurrentqueue.h:2551:8: warning: The struct 'ImplicitProducer' defines member function with name 'dequeue' also defined in its parent struct 'ProducerBase'. [duplInheritedMember]
bowtie2-2.5.4/concurrentqueue.h:1714:15: note: Parent function 'ProducerBase::dequeue'
bowtie2-2.5.4/concurrentqueue.h:2551:8: note: Derived function 'ImplicitProducer::dequeue'
bowtie2-2.5.4/concurrentqueue.h:2780:10: warning: The struct 'ImplicitProducer' defines member function with name 'dequeue_bulk' also defined in its parent struct 'ProducerBase'. [duplInheritedMember]
bowtie2-2.5.4/concurrentqueue.h:1725:17: note: Parent function 'ProducerBase::dequeue_bulk'
bowtie2-2.5.4/concurrentqueue.h:2780:10: note: Derived function 'ImplicitProducer::dequeue_bulk'
bowtie2-2.5.4/pat.h:143:2: style: Struct 'PerThreadReadBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/pat.h:1415:2: style: Class 'PatternSourceReadAhead' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/concurrentqueue.h:2423:3: style: Struct 'ImplicitProducer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/concurrentqueue.h:1453:3: style: Struct 'FreeList < Block >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/pat.h:305:11: style: The destructor '~VectorPatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:238:11: note: Virtual destructor in base class
bowtie2-2.5.4/pat.h:305:11: note: Destructor in derived class
bowtie2-2.5.4/pat.h:313:31: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:247:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:313:31: note: Function in derived class
bowtie2-2.5.4/pat.h:321:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:260:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:321:15: note: Function in derived class
bowtie2-2.5.4/pat.h:330:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:330:15: note: Function in derived class
bowtie2-2.5.4/pat.h:387:11: style: The destructor '~CFilePatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:238:11: note: Virtual destructor in base class
bowtie2-2.5.4/pat.h:387:11: note: Destructor in derived class
bowtie2-2.5.4/pat.h:416:31: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:247:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:416:31: note: Function in derived class
bowtie2-2.5.4/pat.h:425:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:260:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:425:15: note: Function in derived class
bowtie2-2.5.4/pat.h:571:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:425:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:571:15: note: Function in derived class
bowtie2-2.5.4/pat.h:579:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:579:15: note: Function in derived class
bowtie2-2.5.4/pat.h:586:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:438:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:586:31: note: Function in derived class
bowtie2-2.5.4/pat.h:606:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:446:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:606:15: note: Function in derived class
bowtie2-2.5.4/pat.h:633:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:633:15: note: Function in derived class
bowtie2-2.5.4/pat.h:640:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:438:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:640:31: note: Function in derived class
bowtie2-2.5.4/pat.h:679:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:679:15: note: Function in derived class
bowtie2-2.5.4/pat.h:686:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:438:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:686:31: note: Function in derived class
bowtie2-2.5.4/pat.h:717:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:425:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:717:15: note: Function in derived class
bowtie2-2.5.4/pat.h:725:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:725:15: note: Function in derived class
bowtie2-2.5.4/pat.h:732:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:438:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:732:31: note: Function in derived class
bowtie2-2.5.4/pat.h:740:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:446:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:740:15: note: Function in derived class
bowtie2-2.5.4/pat.h:782:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:425:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:782:15: note: Function in derived class
bowtie2-2.5.4/pat.h:790:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:790:15: note: Function in derived class
bowtie2-2.5.4/pat.h:797:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:438:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:797:31: note: Function in derived class
bowtie2-2.5.4/pat.h:805:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:446:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:805:15: note: Function in derived class
bowtie2-2.5.4/pat.h:871:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:425:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:871:15: note: Function in derived class
bowtie2-2.5.4/pat.h:879:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:879:15: note: Function in derived class
bowtie2-2.5.4/pat.h:881:3: style: The destructor '~BAMPatternSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:387:11: note: Virtual destructor in base class
bowtie2-2.5.4/pat.h:881:3: note: Destructor in derived class
bowtie2-2.5.4/pat.h:887:31: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:416:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:887:31: note: Function in derived class
bowtie2-2.5.4/pat.h:894:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:446:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:894:15: note: Function in derived class
bowtie2-2.5.4/pat.h:901:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:438:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:901:31: note: Function in derived class
bowtie2-2.5.4/pat.h:933:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:425:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:933:15: note: Function in derived class
bowtie2-2.5.4/pat.h:941:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:255:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:941:15: note: Function in derived class
bowtie2-2.5.4/pat.h:948:31: style: The function 'nextBatchFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:438:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:948:31: note: Function in derived class
bowtie2-2.5.4/pat.h:956:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:446:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:956:15: note: Function in derived class
bowtie2-2.5.4/pat.h:1037:11: style: The destructor '~SoloPatternComposer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:973:11: note: Virtual destructor in base class
bowtie2-2.5.4/pat.h:1037:11: note: Destructor in derived class
bowtie2-2.5.4/pat.h:1046:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:975:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:1046:15: note: Function in derived class
bowtie2-2.5.4/pat.h:1060:31: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:980:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:1060:31: note: Function in derived class
bowtie2-2.5.4/pat.h:1065:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:985:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:1065:15: note: Function in derived class
bowtie2-2.5.4/pat.h:1106:11: style: The destructor '~DualPatternComposer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:973:11: note: Virtual destructor in base class
bowtie2-2.5.4/pat.h:1106:11: note: Destructor in derived class
bowtie2-2.5.4/pat.h:1117:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:975:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:1117:15: note: Function in derived class
bowtie2-2.5.4/pat.h:1134:31: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:980:31: note: Virtual function in base class
bowtie2-2.5.4/pat.h:1134:31: note: Function in derived class
bowtie2-2.5.4/pat.h:1139:15: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:985:15: note: Virtual function in base class
bowtie2-2.5.4/pat.h:1139:15: note: Function in derived class
bowtie2-2.5.4/pat.h:1363:12: style: The destructor '~LockedPSQueue' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:1330:12: note: Virtual destructor in base class
bowtie2-2.5.4/pat.h:1363:12: note: Destructor in derived class
bowtie2-2.5.4/pat.h:1376:12: style: The destructor '~LockedREQueue' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/pat.h:1330:12: note: Virtual destructor in base class
bowtie2-2.5.4/pat.h:1376:12: note: Destructor in derived class
bowtie2-2.5.4/concurrentqueue.h:1788:4: style: The destructor '~ExplicitProducer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/concurrentqueue.h:1711:12: note: Virtual destructor in base class
bowtie2-2.5.4/concurrentqueue.h:1788:4: note: Destructor in derived class
bowtie2-2.5.4/concurrentqueue.h:2431:4: style: The destructor '~ImplicitProducer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bowtie2-2.5.4/concurrentqueue.h:1711:12: note: Virtual destructor in base class
bowtie2-2.5.4/concurrentqueue.h:2431:4: note: Destructor in derived class
bowtie2-2.5.4/pat.cpp:702:18: style: Condition 'endi>0' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/pat.cpp:691:11: note: Assuming that condition 'endi<1' is not redundant
bowtie2-2.5.4/pat.cpp:702:18: note: Condition 'endi>0' is always true
bowtie2-2.5.4/pat.cpp:1554:18: style: Condition 'endi>0' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/pat.cpp:1543:11: note: Assuming that condition 'endi<1' is not redundant
bowtie2-2.5.4/pat.cpp:1554:18: note: Condition 'endi>0' is always true
bowtie2-2.5.4/concurrentqueue.h:2263:22: style: Condition 'actualCount<desiredCount' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/concurrentqueue.h:2262:18: note: actualCount is assigned 'desiredCount<actualCount?desiredCount:actualCount' here.
bowtie2-2.5.4/concurrentqueue.h:2263:22: note: Condition 'actualCount<desiredCount' is always false
bowtie2-2.5.4/concurrentqueue.h:2795:22: style: Condition 'actualCount<desiredCount' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/concurrentqueue.h:2794:18: note: actualCount is assigned 'desiredCount<actualCount?desiredCount:actualCount' here.
bowtie2-2.5.4/concurrentqueue.h:2795:22: note: Condition 'actualCount<desiredCount' is always false
bowtie2-2.5.4/concurrentqueue.h:3586:8: style: Condition '!raw' is always false [knownConditionTrueFalse]
bowtie2-2.5.4/concurrentqueue.h:3585:16: note: Assignment 'raw=(ConcurrentQueueDefaultTraits::malloc)(size+alignment-1+sizeof(void*))', assigned value is greater than 7
bowtie2-2.5.4/concurrentqueue.h:3586:8: note: Condition '!raw' is always false
bowtie2-2.5.4/pat.cpp:1284:14: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/pat.cpp:1291:30: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/pat.cpp:999:4: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/pat.cpp:994:8: note: c is initialized
bowtie2-2.5.4/pat.cpp:999:4: note: c is overwritten
bowtie2-2.5.4/concurrentqueue.h:3370:6: style: 'continue' is redundant since it is the last statement in a loop. [redundantContinue]
bowtie2-2.5.4/concurrentqueue.h:3380:6: style: 'continue' is redundant since it is the last statement in a loop. [redundantContinue]
bowtie2-2.5.4/pat.cpp:1667:6: style: The scope of the variable 'c' can be reduced. [variableScope]
bowtie2-2.5.4/pat.cpp:458:2: style: Unsigned expression 'nread' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/concurrentqueue.h:3702:58: style:inconclusive: Function 'ConsumerToken' argument 1 names different: declaration 'q' definition 'queue'. [funcArgNamesDifferent]
bowtie2-2.5.4/concurrentqueue.h:719:53: note: Function 'ConsumerToken' argument 1 names different: declaration 'q' definition 'queue'.
bowtie2-2.5.4/concurrentqueue.h:3702:58: note: Function 'ConsumerToken' argument 1 names different: declaration 'q' definition 'queue'.
bowtie2-2.5.4/concurrentqueue.h:3710:66: style:inconclusive: Function 'ConsumerToken' argument 1 names different: declaration 'q' definition 'queue'. [funcArgNamesDifferent]
bowtie2-2.5.4/concurrentqueue.h:722:61: note: Function 'ConsumerToken' argument 1 names different: declaration 'q' definition 'queue'.
bowtie2-2.5.4/concurrentqueue.h:3710:66: note: Function 'ConsumerToken' argument 1 names different: declaration 'q' definition 'queue'.
bowtie2-2.5.4/pat.cpp:770:25: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:589:12: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:770:25: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:823:38: style:inconclusive: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:579:27: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/pat.cpp:823:38: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/pat.cpp:904:25: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:735:12: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:904:25: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:1046:25: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:800:12: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:1046:25: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:1125:38: style:inconclusive: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:790:27: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/pat.cpp:1125:38: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/pat.cpp:1259:56: style:inconclusive: Function 'nextBGZFBlockFromFile' argument 1 names different: declaration 'block' definition 'b'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:889:39: note: Function 'nextBGZFBlockFromFile' argument 1 names different: declaration 'block' definition 'b'.
bowtie2-2.5.4/pat.cpp:1259:56: note: Function 'nextBGZFBlockFromFile' argument 1 names different: declaration 'block' definition 'b'.
bowtie2-2.5.4/pat.cpp:1502:25: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:643:12: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:1502:25: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:1636:14: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:951:12: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:1636:14: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/pat.cpp:1664:36: style:inconclusive: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:941:27: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/pat.cpp:1664:36: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/pat.cpp:631:15: style: Local variable 'i' shadows outer variable [shadowVariable]
bowtie2-2.5.4/pat.cpp:611:13: note: Shadowed declaration
bowtie2-2.5.4/pat.cpp:631:15: note: Shadow variable
bowtie2-2.5.4/pat.h:1356:48: style: Parameter 'psfact' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/concurrentqueue.h:2039:7: warning:inconclusive: Access of moved variable 'el'. [accessMoved]
bowtie2-2.5.4/concurrentqueue.h:2038:17: note: Calling std::move(el)
bowtie2-2.5.4/concurrentqueue.h:2039:7: note: Access of moved variable 'el'.
bowtie2-2.5.4/concurrentqueue.h:2291:9: warning:inconclusive: Access of moved variable 'el'. [accessMoved]
bowtie2-2.5.4/concurrentqueue.h:2290:24: note: Calling std::move(el)
bowtie2-2.5.4/concurrentqueue.h:2291:9: note: Access of moved variable 'el'.
bowtie2-2.5.4/concurrentqueue.h:2301:10: warning:inconclusive: Access of moved variable 'el'. [accessMoved]
bowtie2-2.5.4/concurrentqueue.h:2299:23: note: Calling std::move(el)
bowtie2-2.5.4/concurrentqueue.h:2301:10: note: Access of moved variable 'el'.
bowtie2-2.5.4/concurrentqueue.h:2597:7: warning:inconclusive: Access of moved variable 'el'. [accessMoved]
bowtie2-2.5.4/concurrentqueue.h:2596:17: note: Calling std::move(el)
bowtie2-2.5.4/concurrentqueue.h:2597:7: note: Access of moved variable 'el'.
bowtie2-2.5.4/concurrentqueue.h:2818:9: warning:inconclusive: Access of moved variable 'el'. [accessMoved]
bowtie2-2.5.4/concurrentqueue.h:2817:24: note: Calling std::move(el)
bowtie2-2.5.4/concurrentqueue.h:2818:9: note: Access of moved variable 'el'.
bowtie2-2.5.4/concurrentqueue.h:2828:10: warning:inconclusive: Access of moved variable 'el'. [accessMoved]
bowtie2-2.5.4/concurrentqueue.h:2826:23: note: Calling std::move(el)
bowtie2-2.5.4/concurrentqueue.h:2828:10: note: Access of moved variable 'el'.
bowtie2-2.5.4/pat.cpp:1048:8: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/pat.cpp:1667:8: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/read_qseq.cpp:74:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/read_qseq.cpp:142:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ref_read.cpp:50:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ref_read.cpp:191:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ref_read.cpp:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ref_read.cpp:298:2: style: Unsigned expression 'bothTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/ref_read.cpp:299:2: style: Unsigned expression 'unambigTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
bowtie2-2.5.4/ref_read.cpp:143:7: style: Variable 'lc' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
bowtie2-2.5.4/bt2_search.cpp:4596:9: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
bowtie2-2.5.4/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_oldM' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_newM' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_oldS' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_newS' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/bt2_search.cpp:1887:2: warning: Member variable 'PerfMetrics::lastElapsed' is not initialized in the constructor. [uninitMemberVar]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < pair < int , string > , 128 >::cat_' is not assigned a value in 'EList < pair < int , string > , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/ds.h:394:15: warning: Member variable 'EList < std :: thread * , 128 >::cat_' is not assigned a value in 'EList < std :: thread * , 128 >::operator='. [operatorEqVarError]
bowtie2-2.5.4/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]
bowtie2-2.5.4/reference.cpp:55:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/reference.cpp:333:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/reference.cpp:376:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/reference.cpp:444:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/reference.cpp:602:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < pair < int , string > , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/ds.h:702:18: performance:inconclusive: Technically the member function 'EList < pair < int , string > , 128 >::front' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < std :: thread * , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/ds.h:532:7: style:inconclusive: Technically the member function 'EList < thread_tracking_pair , 128 >::fillZero' can be const. [functionConst]
bowtie2-2.5.4/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]
bowtie2-2.5.4/bt2_search.h:27:2: style: Class 'multiseedSearchWorker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/bt2_search.h:36:2: style: Class 'multiseedSearchWorker_2p5' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bowtie2-2.5.4/read_qseq.cpp:135:4: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization]
bowtie2-2.5.4/read_qseq.cpp:88:8: note: c is initialized
bowtie2-2.5.4/read_qseq.cpp:135:4: note: c is overwritten
bowtie2-2.5.4/read_qseq.cpp:35:6: style: The scope of the variable 'c' can be reduced. [variableScope]
bowtie2-2.5.4/read_qseq.cpp:56:25: style:inconclusive: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:689:12: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/read_qseq.cpp:56:25: note: Function 'nextBatchFromFile' argument 3 names different: declaration 'read_idx' definition 'readi'.
bowtie2-2.5.4/read_qseq.cpp:83:37: style:inconclusive: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'. [funcArgNamesDifferent]
bowtie2-2.5.4/pat.h:679:27: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/read_qseq.cpp:83:37: note: Function 'parse' argument 1 names different: declaration 'ra' definition 'r'.
bowtie2-2.5.4/read_qseq.cpp:29:14: style: Parameter 'buf' can be declared as reference to const [constParameterReference]
bowtie2-2.5.4/aligner_metrics.h:201:27: style: Condition 'ent<0.75f' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_metrics.h:200:16: note: Assignment 'ent=0.0f', assigned value is 0.0
bowtie2-2.5.4/aligner_metrics.h:201:27: note: Condition 'ent<0.75f' is always true
bowtie2-2.5.4/aligner_metrics.h:202:25: style: Condition 'ent<0.001f' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/aligner_metrics.h:200:16: note: Assignment 'ent=0.0f', assigned value is 0.0
bowtie2-2.5.4/aligner_metrics.h:202:25: note: Condition 'ent<0.001f' is always true
bowtie2-2.5.4/bt2_search.cpp:1530:18: style: Condition 'args.size()>=1' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/bt2_search.cpp:1525:37: note: Assuming that condition 'args.size()==0' is not redundant
bowtie2-2.5.4/bt2_search.cpp:1530:18: note: Condition 'args.size()>=1' is always true
bowtie2-2.5.4/bt2_search.cpp:4561:3: error: Memory leak: fname [memleak]
bowtie2-2.5.4/bt2_search.cpp:4566:3: error: Memory leak: fname [memleak]
bowtie2-2.5.4/bt2_search.cpp:3013:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:4163:28: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:4516:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:4550:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:4580:16: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:4652:50: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:4778:66: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:4780:62: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/reference.cpp:203:5: warning: Class 'BitPairReference' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bowtie2-2.5.4/reference.cpp:203:5: warning: Class 'BitPairReference' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bowtie2-2.5.4/sstring.h:2938:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2851. Dynamic binding is not used. [virtualCallInConstructor]
bowtie2-2.5.4/sstring.h:2851:4: note: Calling install
bowtie2-2.5.4/sstring.h:2938:15: note: install is a virtual function
bowtie2-2.5.4/reference.cpp:409:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/reference.cpp:404:12: note: Assuming that condition 'count==0' is not redundant
bowtie2-2.5.4/reference.cpp:409:14: note: Condition 'count>0' is always true
bowtie2-2.5.4/reference.cpp:573:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
bowtie2-2.5.4/reference.cpp:567:12: note: Assuming that condition 'count==0' is not redundant
bowtie2-2.5.4/reference.cpp:573:14: note: Condition 'count>0' is always true
bowtie2-2.5.4/reference.cpp:65:3: error: Resource leak: f3 [resourceLeak]
bowtie2-2.5.4/reference.cpp:107:4: error: Resource leak: f4 [resourceLeak]
bowtie2-2.5.4/reference.cpp:118:3: error: Resource leak: f4 [resourceLeak]
bowtie2-2.5.4/reference.cpp:304:22: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/reference.cpp:373:18: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/reference.cpp:430:18: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/reference.cpp:438:13: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/reference.cpp:510:9: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/bt2_search.cpp:934:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bowtie2-2.5.4/reference.cpp:434:6: style: The scope of the variable 'off2' can be reduced. [variableScope]
bowtie2-2.5.4/reference.cpp:217:10: style: Local variable 'f4' shadows outer variable [shadowVariable]
bowtie2-2.5.4/reference.cpp:53:13: note: Shadowed declaration
bowtie2-2.5.4/reference.cpp:217:10: note: Shadow variable
bowtie2-2.5.4/reference.cpp:275:31: style: Local variable 'tmp_destU32_' shadows outer variable [shadowVariable]
bowtie2-2.5.4/reference.h:186:2: note: Shadowed declaration
bowtie2-2.5.4/reference.cpp:275:31: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:3017:33: style: The scope of the variable 'readahead_factory' can be reduced. [variableScope]
bowtie2-2.5.4/bt2_search.cpp:3022:26: style: The scope of the variable 'msink' can be reduced. [variableScope]
bowtie2-2.5.4/reference.cpp:205:28: style: Variable 'e' can be declared as reference to const [constVariableReference]
bowtie2-2.5.4/reference.cpp:53:13: style: Variable 'f4' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/reference.cpp:433:11: style: Variable 'dest_2' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/bt2_search.cpp:4579:17: style: The scope of the variable 'ent' can be reduced. [variableScope]
bowtie2-2.5.4/reference.cpp:453:17: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:1351:10: style: Local variable 'argstr' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:4811:15: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:1351:10: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:1363:10: style: Local variable 'argstr' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:4811:15: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:1363:10: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:3414:11: style: Local variable 'done' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:3162:8: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:3414:11: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:3468:12: style: Local variable 'ret' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:3168:21: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:3468:12: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:3650:12: style: Local variable 'ret' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:3168:21: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:3650:12: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:3926:13: style: Local variable 'ret' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:3168:21: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:3926:13: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:4729:9: style: Local variable '_t' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:4692:9: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:4729:9: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:4742:9: style: Local variable '_t' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:4692:9: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:4742:9: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:4761:9: style: Local variable '_t' shadows outer variable [shadowVariable]
bowtie2-2.5.4/bt2_search.cpp:4692:9: note: Shadowed declaration
bowtie2-2.5.4/bt2_search.cpp:4761:9: note: Shadow variable
bowtie2-2.5.4/sam.cpp:195:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.cpp:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.cpp:80:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/scoring.cpp:107:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:3247:13: style: Variable 'rdlens' can be declared as const array [constVariable]
bowtie2-2.5.4/bt2_search.cpp:3248:13: style: Variable 'rdrows' can be declared as const array [constVariable]
bowtie2-2.5.4/bt2_search.cpp:3778:10: style: Variable 'seedlens' can be declared as const array [constVariable]
bowtie2-2.5.4/bt2_search.cpp:4342:11: style: Variable 'rdlens' can be declared as const array [constVariable]
bowtie2-2.5.4/bt2_search.cpp:4579:17: style: Variable 'ent' can be declared as pointer to const [constVariablePointer]
bowtie2-2.5.4/simple_func.cpp:36:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/bt2_search.cpp:2780:20: style: struct member 'PerfMetrics::lastElapsed' is never used. [unusedStructMember]
bowtie2-2.5.4/sam.cpp:874:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
bowtie2-2.5.4/sam.h:257:7: performance:inconclusive: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sam.cpp:31:17: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sam.h:257:7: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sam.h:362:7: performance:inconclusive: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sam.cpp:76:17: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sam.h:362:7: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sam.h:409:7: performance:inconclusive: Technically the member function 'SamConfig::printPreservedOptFlags' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sam.cpp:881:17: note: Technically the member function 'SamConfig::printPreservedOptFlags' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sam.h:409:7: note: Technically the member function 'SamConfig::printPreservedOptFlags' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sam.cpp:274:13: style: Local variable 'mn' shadows outer variable [shadowVariable]
bowtie2-2.5.4/sam.cpp:260:12: note: Shadowed declaration
bowtie2-2.5.4/sam.cpp:274:13: note: Shadow variable
bowtie2-2.5.4/sam.cpp:280:13: style: Local variable 'pe' shadows outer variable [shadowVariable]
bowtie2-2.5.4/sam.cpp:266:12: note: Shadowed declaration
bowtie2-2.5.4/sam.cpp:280:13: note: Shadow variable
bowtie2-2.5.4/bt2_search.cpp:4400:14: style: Variable 'nceil[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4415:17: style: Variable 'mtStreak[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4415:31: style: Variable 'mtStreak[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4416:17: style: Variable 'mxDp[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4416:31: style: Variable 'mxDp[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4417:17: style: Variable 'mxUg[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4417:31: style: Variable 'mxUg[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4418:17: style: Variable 'mxIter[0]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4418:31: style: Variable 'mxIter[1]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4422:21: style: Variable 'mtStreak[mate]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4423:21: style: Variable 'mxDp[mate]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4424:21: style: Variable 'mxUg[mate]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/bt2_search.cpp:4425:21: style: Variable 'mxIter[mate]' is assigned a value that is never used. [unreadVariable]
bowtie2-2.5.4/sse_util.h:520:7: performance:inconclusive: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bowtie2-2.5.4/sse_util.cpp:27:20: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sse_util.h:520:7: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
bowtie2-2.5.4/sse_util.cpp:28:11: style: Parameter 'pvH' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/sse_util.cpp:29:11: style: Parameter 'pvE' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/sse_util.cpp:30:11: style: Parameter 'pvF' can be declared as pointer to const [constParameterPointer]
bowtie2-2.5.4/zstd_decompress.cpp:16:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/zstd_decompress.cpp:97:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/zstd_decompress.cpp:132:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/zstd_decompress.cpp:180:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bowtie2-2.5.4/zstd_decompress.cpp:169:2: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled]
bowtie2-2.5.4/zstd_decompress.cpp:14:12: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/zstd_decompress.cpp:98:19: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/zstd_decompress.cpp:110:19: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/zstd_decompress.cpp:153:10: style: C-style pointer casting [cstyleCast]
bowtie2-2.5.4/zstd_decompress.cpp:105:29: style: The scope of the variable 'nread' can be reduced. [variableScope]
bowtie2-2.5.4/zstd_decompress.cpp:142:13: style: The scope of the variable 'ret' can be reduced. [variableScope]
diff:
2.16.0 bowtie2-2.5.4/aligner_bt.cpp:1158:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.cpp:1158:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.cpp:1247:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.cpp:1247:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.cpp:1362:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.cpp:1362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.cpp:1475:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.cpp:1475:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.cpp:54:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.cpp:54:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.cpp:604:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.cpp:604:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:256:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:256:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:408:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:408:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:462:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:462:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:470:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:470:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:478:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:478:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:488:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:488:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:556:41: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable score_st_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:556:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_st_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:592:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:592:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_bt.h:638:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_bt.h:638:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_cache.cpp:31:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_cache.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_cache.cpp:46:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_cache.cpp:46:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_cache.cpp:80:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_cache.cpp:80:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_cache.h:147:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_cache.h:147:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_cache.h:375:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_cache.h:375:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_cache.h:428:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_cache.h:428:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_cache.h:955:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_cache.h:955:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_driver.cpp:305:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_driver.cpp:305:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_driver.cpp:30:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_driver.cpp:30:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_driver.h:198:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_driver.h:198:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_metrics.h:138:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_metrics.h:138:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_metrics.h:201:27: style: Condition 'ent<0.75f' is always true [knownConditionTrueFalse]
     bowtie2-2.5.4/aligner_metrics.h:200:16: note: Assignment 'ent=0.0f', assigned value is 0.0
     bowtie2-2.5.4/aligner_metrics.h:201:27: note: Condition 'ent<0.75f' is always true
head bowtie2-2.5.4/aligner_metrics.h:202:25: style: Condition 'ent<0.001f' is always true [knownConditionTrueFalse]
     bowtie2-2.5.4/aligner_metrics.h:200:16: note: Assignment 'ent=0.0f', assigned value is 0.0
     bowtie2-2.5.4/aligner_metrics.h:202:25: note: Condition 'ent<0.001f' is always true
2.16.0 bowtie2-2.5.4/aligner_result.cpp:105:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:105:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:1063:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:1063:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:209:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:209:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:236:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:236:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:275:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:275:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:365:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:365:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:455:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:455:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:574:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:574:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:660:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:660:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:749:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:749:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:774:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:774:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:788:6: style: Variable 'bufc' can be declared as pointer to const [constVariablePointer]
head bowtie2-2.5.4/aligner_result.cpp:820:23: style: Variable 'bufc' can be declared as pointer to const [constVariablePointer]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:901:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:901:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:939:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:939:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.cpp:992:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.cpp:992:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1069:20: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1069:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1080:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1080:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:117:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:117:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1204:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1204:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1213:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1213:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1224:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1233:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1233:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1243:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1243:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1252:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1252:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1262:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1262:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1282:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1282:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1314:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1314:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1350:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1350:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:150:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:150:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:1521:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:1521:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:206:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:206:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:343:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:343:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:365:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:365:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:730:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:730:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_result.h:824:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_result.h:824:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:101:6: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:101:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:1380:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:1380:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:1480:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:1480:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:1622:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:1622:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:1640:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:1640:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:1773:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:1773:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:1895:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:1895:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:231:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:231:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:513:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:513:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:659:6: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:659:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:738:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:738:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:763:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:763:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:867:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:867:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.cpp:998:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.cpp:998:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:1068:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:1068:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:1112:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:1112:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:1156:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:1156:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:1179:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:1179:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:1188:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:1188:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:1228:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:1228:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:163:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:163:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:176:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:176:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:192:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:205:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:205:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:578:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:578:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:654:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:654:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:694:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:694:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:952:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:952:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:961:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:961:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed.h:988:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed.h:988:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:1000:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:1000:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:1079:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:1079:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:1263:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:1263:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:1342:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:1342:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:155:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pen [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:155:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pen [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:236:26: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:236:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:348:23: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable gapadd_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:348:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gapadd_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:445:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable off5p [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:445:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off5p [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:546:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:546:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:63:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:63:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fw [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.cpp:894:39: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.cpp:894:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1227:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1227:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1275:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1275:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1426:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1426:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1498:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1498:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1635:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1635:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1676:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1676:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1689:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1689:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1917:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1917:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1939:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1939:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:1970:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:1970:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:2159:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable botf [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:2159:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable botf [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:2199:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:2199:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:2418:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:2418:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:2505:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:2505:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:319:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:319:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:536:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:536:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:650:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:650:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed2.h:947:17: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed2.h:947:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed_policy.cpp:326:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed_policy.cpp:326:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_seed_policy.cpp:41:7: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_seed_policy.cpp:41:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw.cpp:173:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw.cpp:173:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw.cpp:303:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw.cpp:303:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw.cpp:43:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw.cpp:43:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw.cpp:504:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw.cpp:504:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw.cpp:743:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw.cpp:743:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw.cpp:91:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw.cpp:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw.h:381:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw.h:381:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.cpp:1441:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.cpp:1441:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.cpp:366:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.cpp:366:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.cpp:538:27: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.cpp:538:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.cpp:78:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.cpp:78:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.cpp:797:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.cpp:797:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.h:198:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.h:198:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.h:224:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.h:224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_driver.h:248:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_driver.h:248:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_nuc.h:209:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_nuc.h:209:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_sw_nuc.h:246:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_sw_nuc.h:246:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.cpp:44:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.cpp:44:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.cpp:68:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.cpp:68:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.cpp:80:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.cpp:80:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:122:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:122:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:134:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:134:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:146:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:146:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:158:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:158:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:170:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:170:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:182:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:182:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:223:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:223:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:441:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:441:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:466:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:466:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse.h:491:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse.h:491:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1207:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1207:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1317:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:1317:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:203:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:203:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:295:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:295:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:781:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:781:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:90:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_i16.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1182:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1182:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1292:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:1292:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:192:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:192:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:296:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:296:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:776:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:776:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:90:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_ee_u8.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1427:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1427:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1624:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:1624:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:203:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:203:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:295:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:295:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:90:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:939:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_i16.cpp:939:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1396:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1396:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1597:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:1597:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:217:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:217:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:307:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:307:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:90:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:90:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:928:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aligner_swsse_loc_u8.cpp:928:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:108:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:108:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:1505:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:1505:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:157:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:157:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:1649:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:1649:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:222:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:222:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:313:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:313:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:334:8: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:334:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:361:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:361:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:699:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:699:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.cpp:74:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.cpp:74:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.h:1055:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.h:1055:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.h:248:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.h:248:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.h:278:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.h:278:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.h:510:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.h:510:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.h:535:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.h:535:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/aln_sink.h:694:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/aln_sink.h:694:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/alphabet.h:119:8: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/alphabet.h:119:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/alphabet.h:91:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/alphabet.h:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/assert_helpers.h:251:7: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/assert_helpers.h:251:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/assert_helpers.h:269:8: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/assert_helpers.h:269:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/binary_sa_search.h:56:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/binary_sa_search.h:56:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bitpack.h:32:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bitpack.h:32:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bitpack.h:38:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bitpack.h:38:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bitpack.h:39:17: error: Shifting by a negative value is undefined behaviour [shiftNegative]
2.16.0 bowtie2-2.5.4/bitpack.h:43:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bitpack.h:43:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bitpack.h:49:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bitpack.h:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:1011:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:1011:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:113:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:113:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:317:21: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:317:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:406:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:406:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:458:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:458:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:524:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:524:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:556:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:556:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:607:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:607:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:632:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:632:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:814:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:814:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:835:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:835:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:876:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:876:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/blockwise_sa.h:908:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/blockwise_sa.h:908:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bowtie_build_main.cpp:63:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bowtie_build_main.cpp:63:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bowtie_main.cpp:62:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bowtie_main.cpp:62:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_build.cpp:125:39: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable BOWTIE2_VERSION [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_build.cpp:125:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BOWTIE2_VERSION [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_build.cpp:223:19: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_build.cpp:223:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_build.cpp:252:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_build.cpp:252:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_build.cpp:356:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_build.cpp:356:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_build.cpp:366:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_build.cpp:366:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_build.cpp:386:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_build.cpp:386:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_dp.cpp:139:113: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_dp.cpp:139:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_dp.cpp:192:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_dp.cpp:192:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_dp.cpp:233:7: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_dp.cpp:233:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_dp.cpp:290:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_dp.cpp:290:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_dp.cpp:487:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_dp.cpp:487:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_dp.cpp:567:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_dp.cpp:567:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_dp.cpp:648:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable opterr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_dp.cpp:648:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable opterr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.cpp:132:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.cpp:132:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.cpp:152:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.cpp:152:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.cpp:184:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.cpp:184:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.cpp:231:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.cpp:231:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.cpp:280:14: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.cpp:280:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.cpp:71:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.cpp:71:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1217:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1217:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1305:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1305:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1381:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1381:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1436:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1436:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1483:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1483:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1546:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1546:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1573:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1573:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1595:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1595:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1636:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1636:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1661:67: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1661:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1764:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1764:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1811:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1811:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:1900:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:1900:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2093:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2093:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:210:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:210:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2141:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2141:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2186:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2186:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:226:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:226:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2280:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2280:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2322:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2322:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2350:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2350:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2384:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2384:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2429:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2429:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2461:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2461:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2479:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2479:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2570:10: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2570:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2634:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2634:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2673:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2673:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable off [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2705:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2705:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:2840:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:2840:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:294:30: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:294:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:3194:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:3194:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:335:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:335:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:377:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:460:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:460:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:621:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:621:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:675:54: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:675:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:890:26: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:890:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_idx.h:998:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_idx.h:998:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_io.cpp:56:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_io.cpp:56:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_io.cpp:644:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_io.cpp:644:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_io.cpp:732:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_io.cpp:732:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_io.cpp:743:57: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_io.cpp:743:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_io.cpp:837:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_io.cpp:837:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_io.cpp:884:36: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_io.cpp:884:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_io.cpp:938:13: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_io.cpp:938:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_locks.cpp:16:27: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_locks.cpp:16:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_locks.cpp:30:32: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_locks.cpp:30:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_locks.cpp:35:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_locks.cpp:35:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_locks.cpp:6:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_locks.cpp:6:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_locks.h:59:26: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_locks.h:59:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_locks.h:65:27: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_locks.h:65:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:1025:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:1025:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:1612:21: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:1612:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:2715:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:2715:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:274:8: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:274:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:2800:57: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:2800:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:2818:51: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:2818:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:2836:37: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:2836:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:2855:37: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:2855:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:2913:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:2913:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:3083:51: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:3083:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4228:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4228:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4506:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4506:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4519:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4519:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4543:7: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4543:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4583:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4583:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4653:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4653:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4692:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4692:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:4820:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:4820:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:690:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:690:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:719:39: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable BOWTIE2_VERSION [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:719:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BOWTIE2_VERSION [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:925:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:925:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_search.cpp:985:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_search.cpp:985:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_util.cpp:151:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_util.cpp:151:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_util.cpp:203:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_util.cpp:203:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_util.cpp:47:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_util.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/bt2_util.cpp:87:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/bt2_util.cpp:87:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1132:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1132:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1170:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1170:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1191:113: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1191:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1234:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1234:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1251:113: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1251:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1328:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1328:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1342:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1342:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1369:110: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1369:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1376:102: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1376:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1382:115: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1382:115: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1389:107: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1389:107: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1395:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1395:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1453:138: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1453:138: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1466:65: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1466:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acq_rel [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1478:39: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1478:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1513:58: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1513:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1526:39: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1526:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1572:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1572:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1572:40: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable explicit_context [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1572:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable explicit_context [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1599:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1599:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1618:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1618:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1639:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1639:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1654:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1654:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable context [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1739:36: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1739:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1744:63: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1744:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1796:36: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1796:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1851:57: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1851:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:1957:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:1957:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2060:55: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2060:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2250:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2250:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2362:120: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2362:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2446:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2446:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2489:57: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2489:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2554:45: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2554:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2587:43: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2587:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2637:55: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2637:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2782:42: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2782:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2903:48: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2903:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2937:48: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2937:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2954:43: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2954:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:2968:37: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:2968:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3058:39: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3058:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3108:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3108:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable canAlloc [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3233:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3233:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3253:35: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3253:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3284:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3284:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3303:34: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3303:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3338:44: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3338:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3364:39: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3364:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3407:50: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3407:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_acquire [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3581:55: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3581:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3597:55: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3597:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3607:51: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3607:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3630:38: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3630:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3637:38: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3637:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable U [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3705:65: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3705:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:3713:114: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:3713:114: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:479:38: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:479:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:488:55: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:488:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:495:38: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:495:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:512:37: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:512:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:699:40: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:699:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_release [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:820:51: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:820:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:844:51: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:844:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:861:41: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:861:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/concurrentqueue.h:922:51: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/concurrentqueue.h:922:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:127:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:127:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:156:13: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:156:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:170:6: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:170:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:297:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:297:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:336:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:336:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:399:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:399:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:423:31: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:423:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:435:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:435:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:470:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:470:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:531:10: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:531:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:573:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:573:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:614:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:614:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:706:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:706:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TStr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:721:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:721:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:746:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:746:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:87:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:87:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:920:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:920:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:931:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:931:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:950:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:950:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/diff_sample.h:993:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/diff_sample.h:993:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/dp_framer.cpp:191:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/dp_framer.cpp:191:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/dp_framer.cpp:305:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/dp_framer.cpp:305:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/dp_framer.cpp:91:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/dp_framer.cpp:91:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/dp_framer.h:109:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/dp_framer.h:109:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.cpp:44:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.cpp:44:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1001:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1001:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1050:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1050:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1059:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1059:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1079:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1079:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1094:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1094:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1119:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1119:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1179:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1179:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1187:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1187:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1195:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1195:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1208:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1216:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:122:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:122:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1259:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1259:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1289:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1289:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1330:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1330:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1353:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1353:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1394:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1394:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1403:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1403:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1423:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1423:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1438:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1438:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1461:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1461:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1519:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1519:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1527:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1527:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1535:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1535:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1548:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1548:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1556:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1556:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1599:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1599:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1629:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1629:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1670:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1670:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1693:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1693:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1739:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1739:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1751:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1751:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1764:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1764:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1786:38: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1786:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1793:37: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1793:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1897:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1897:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1924:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1924:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:1972:6: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:1972:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2015:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2015:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2032:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2032:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2079:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2079:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2088:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2088:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2108:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2108:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2123:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2123:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2148:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2148:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2208:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2216:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2224:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2224:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2237:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2237:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2245:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2245:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2293:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2293:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2323:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2323:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2361:8: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2361:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2364:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2364:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2384:8: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2384:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2387:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2387:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2432:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2432:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2515:44: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2515:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2534:26: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2534:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2558:32: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2558:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2575:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2575:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2598:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2598:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2627:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2627:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2646:6: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2646:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2688:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2688:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2705:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2705:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2938:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2938:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:2946:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:2946:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3137:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3137:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3176:14: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3176:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3180:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3180:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3193:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3193:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3197:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3197:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3216:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3216:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3220:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3220:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3234:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3234:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3238:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3238:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3260:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3260:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3260:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3260:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3269:21: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3269:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3283:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3283:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3293:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3293:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3305:30: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3305:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3307:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3307:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3316:30: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3316:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3318:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3318:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3328:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3328:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3328:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3328:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3350:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3350:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3411:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3411:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3431:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3431:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3440:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3440:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3449:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3449:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3458:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3458:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3482:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3482:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3543:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3543:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:355:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:355:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3563:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3563:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3572:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3572:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3581:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3581:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3590:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3590:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3614:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3614:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:364:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:364:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:383:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:383:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3855:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3855:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3892:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3892:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3944:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3944:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:395:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:395:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:3964:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:3964:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:4169:20: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:4169:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:421:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:421:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:513:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:513:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:533:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:533:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:592:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:592:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:603:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:603:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:619:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:619:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:633:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:633:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:649:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:649:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:665:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:665:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:687:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:687:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:695:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:695:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:750:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:750:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:758:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:758:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:796:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:796:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:805:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:805:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:841:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:841:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:85:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:85:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:866:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:866:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:886:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:886:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:912:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:912:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ds.h:938:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ds.h:938:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:129:44: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:129:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:206:44: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:206:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:302:44: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:302:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:378:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:378:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:416:14: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:416:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:441:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:441:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:456:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:456:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/edit.cpp:66:19: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/edit.cpp:66:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/endian_swap.h:118:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/endian_swap.h:118:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/endian_swap.h:137:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/endian_swap.h:137:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:118:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:118:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:242:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:242:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:270:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:377:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:391:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:391:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:409:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:409:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:567:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:567:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:578:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:578:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:607:10: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:607:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:641:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:641:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:660:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:660:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:692:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:692:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:754:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:754:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:772:14: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:772:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:844:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:844:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/filebuf.h:960:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/filebuf.h:960:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:1174:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:1174:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:1229:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:1229:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:1264:67: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:1264:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:1270:71: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:1270:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:362:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:395:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:395:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:404:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:404:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:412:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:412:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:463:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:463:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:498:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:498:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:727:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:727:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:748:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:748:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:759:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:759:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:780:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:780:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:795:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:795:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:806:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:806:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:844:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:844:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/group_walk.h:878:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/group_walk.h:878:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ival_list.h:147:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ival_list.h:147:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ival_list.h:182:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ival_list.h:182:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ival_list.h:234:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ival_list.h:234:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ival_list.h:270:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ival_list.h:270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ival_list.h:62:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ival_list.h:62:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ival_list.h:94:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ival_list.h:94:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/mask.h:57:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/mask.h:57:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:1049:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:1049:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:106:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:106:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:1146:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:1146:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:124:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:124:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:157:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:157:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:176:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:267:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:267:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:306:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:306:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:324:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:324:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:350:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:350:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:38:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:38:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:412:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:412:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:48:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:48:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:493:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:493:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:527:46: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:527:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:656:13: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:656:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:680:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:680:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:711:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:711:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:776:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:776:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:808:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:808:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/multikey_qsort.h:901:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/multikey_qsort.h:901:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/outq.cpp:31:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/outq.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/outq.cpp:63:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/outq.cpp:63:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1004:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1004:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1052:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1052:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:108:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:108:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1138:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1138:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1263:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1263:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1550:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1550:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:163:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:163:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1680:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1680:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1711:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1711:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1719:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1719:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:1725:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:1725:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:213:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:213:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:253:5: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:253:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:330:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:330:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:458:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:458:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:502:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:502:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:59:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:59:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:614:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:614:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:652:18: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable readOrigBuf [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:652:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readOrigBuf [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:698:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:698:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:776:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:776:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:853:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:853:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.cpp:957:19: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable readOrigBuf [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.cpp:957:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable readOrigBuf [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:1092:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:1092:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:164:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:164:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:184:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:184:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:192:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:377:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:377:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:486:10: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:486:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:504:30: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:504:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pat.h:712:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pat.h:712:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pe.cpp:178:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pe.cpp:178:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pe.cpp:46:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pe.cpp:46:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pe.h:118:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pe.h:118:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/pe.h:159:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/pe.h:159:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/presets.cpp:93:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/presets.cpp:93:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/qual.h:108:8: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/qual.h:108:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/qual.h:166:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/qual.h:166:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/qual.h:197:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/qual.h:197:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/qual.h:226:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/qual.h:226:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/qual.h:46:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/qual.h:46:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/random_util.h:130:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/random_util.h:130:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/read.h:208:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/read.h:208:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/read.h:220:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/read.h:220:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/read.h:229:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/read.h:229:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/read.h:241:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/read.h:241:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/read.h:318:14: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable alignment [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/read.h:318:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alignment [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/read_qseq.cpp:142:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/read_qseq.cpp:142:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/read_qseq.cpp:74:11: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/read_qseq.cpp:74:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ref_coord.h:243:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ref_coord.h:243:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ref_coord.h:408:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ref_coord.h:408:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ref_read.cpp:191:53: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ref_read.cpp:191:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ref_read.cpp:258:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ref_read.cpp:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ref_read.cpp:50:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ref_read.cpp:50:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ref_read.h:167:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ref_read.h:167:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/ref_read.h:82:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/ref_read.h:82:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/reference.cpp:333:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/reference.cpp:333:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/reference.cpp:376:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/reference.cpp:376:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/reference.cpp:444:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/reference.cpp:444:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/reference.cpp:55:6: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/reference.cpp:55:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/reference.cpp:602:38: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/reference.cpp:602:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/reference.h:132:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/reference.h:132:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sam.cpp:195:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sam.cpp:195:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sam.h:159:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sam.h:159:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sam.h:167:25: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sam.h:167:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sam.h:471:44: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sam.h:471:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.cpp:107:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.cpp:107:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.cpp:49:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.cpp:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.cpp:80:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.cpp:80:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.h:114:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.h:114:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.h:209:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.h:209:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.h:286:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.h:286:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.h:303:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.h:303:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.h:330:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.h:330:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.h:341:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.h:341:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/scoring.h:352:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/scoring.h:352:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sequence_io.h:45:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sequence_io.h:45:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sequence_io.h:75:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sequence_io.h:75:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/simple_func.cpp:36:7: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/simple_func.cpp:36:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:152:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:152:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:160:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:160:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:207:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:222:9: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:222:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:314:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:314:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:368:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:368:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:38:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:38:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:444:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:444:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:459:35: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:459:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sse_util.h:481:57: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sse_util.h:481:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sc [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1056:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1056:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1073:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1073:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1091:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1091:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1121:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1121:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1129:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1129:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1137:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1137:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:119:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:119:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1450:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1450:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1480:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1480:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1526:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1526:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:153:31: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:153:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1547:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1547:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1625:6: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable I [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1625:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable I [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1714:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1714:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1730:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1730:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::cs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::len_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::printcs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 0 >::sz_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::cs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::len_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::printcs_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < char , 1024 , 2 , 1024 >::sz_' is not assigned a value in 'SStringExpandable < char , 1024 , 2 , 1024 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::cs_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::len_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::printcs_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::sz_' is not assigned a value in 'SStringExpandable < uint32_t , 1024 , 2 , 0 >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::cs_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::len_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::printcs_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:1739:30: warning: Member variable 'SStringExpandable::sz_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
2.16.0 bowtie2-2.5.4/sstring.h:1756:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1756:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:176:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:176:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1771:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1771:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1779:45: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1779:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1787:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1787:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1799:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1799:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1807:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1807:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1815:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1815:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1823:35: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1823:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1839:35: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1839:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1851:43: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1851:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1915:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1915:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1931:35: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1931:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1940:35: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1940:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1953:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1953:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1970:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1970:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:1997:47: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:1997:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:202:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:202:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2037:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2037:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2053:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2053:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2087:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2087:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2184:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2184:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2192:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2192:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2207:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2223:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2223:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2249:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2249:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2263:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2263:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2271:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2271:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2279:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2279:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2291:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2291:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:229:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:229:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2306:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2306:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2318:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2318:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2382:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2382:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2398:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2398:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2407:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2407:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2420:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2420:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2437:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2437:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2459:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2459:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2512:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2512:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:256:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:256:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2611:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2611:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2624:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2624:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2636:32: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2636:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2654:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2654:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2670:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2670:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2685:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2685:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2715:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2715:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2725:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2725:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2735:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2735:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2744:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2744:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2753:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2753:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2769:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2769:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:277:31: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:277:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2785:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2785:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2802:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2802:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2896:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2896:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2909:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2909:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2921:32: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2921:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2958:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2958:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2973:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2973:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:2987:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:2987:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3016:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3016:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:301:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:301:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3025:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3025:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3036:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3036:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3045:12: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3045:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3056:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3056:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3071:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3071:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3086:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3086:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3103:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3103:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3168:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3168:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3183:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3183:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3197:32: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3197:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3215:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3215:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3231:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3231:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3254:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3254:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3263:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3263:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3274:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3274:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:327:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:327:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3283:15: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3283:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sz_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3294:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3294:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cs_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3316:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3316:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3325:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3325:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3340:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3340:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3357:28: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3357:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:3378:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:3378:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:348:31: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:348:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:372:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:372:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:398:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:398:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:419:31: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:419:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:443:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:443:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:469:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:469:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString < char >::cs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString < char >::len_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString < char >::printcs_' is not assigned a value in 'SString < char >::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString::cs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString::len_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
head bowtie2-2.5.4/sstring.h:583:14: warning: Member variable 'SString::printcs_' is not assigned a value in 'SString::operator='. [operatorEqVarError]
2.16.0 bowtie2-2.5.4/sstring.h:625:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:625:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:641:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:641:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:652:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:652:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:660:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:660:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:668:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:668:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:676:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:676:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:687:30: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:687:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:698:38: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:698:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:786:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:786:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:800:3: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:800:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:841:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:841:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/sstring.h:94:31: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/sstring.h:94:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T1 [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/timer.h:141:47: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/timer.h:141:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/timer.h:165:21: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/timer.h:165:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/tokenize.h:45:17: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/tokenize.h:45:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/unique.h:124:22: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/unique.h:124:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/unique.h:198:4: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/unique.h:198:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/unique.h:442:21: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/unique.h:442:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/unique.h:62:9: style: Parameter 'inps' can be declared as pointer to const [constParameterPointer]
2.16.0 bowtie2-2.5.4/unique.h:65:11: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/unique.h:65:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score_ [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/util.h:34:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable is_signed [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/util.h:34:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_signed [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/word_io.h:124:30: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/word_io.h:124:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/word_io.h:160:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/word_io.h:160:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/word_io.h:195:30: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/word_io.h:195:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/word_io.h:48:36: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/word_io.h:48:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/word_io.h:59:36: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/word_io.h:59:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/word_io.h:68:36: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/word_io.h:68:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/word_io.h:89:29: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/word_io.h:89:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/zbox.h:41:2: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/zbox.h:41:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/zstd_decompress.cpp:132:31: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/zstd_decompress.cpp:132:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/zstd_decompress.cpp:16:20: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/zstd_decompress.cpp:16:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/zstd_decompress.cpp:180:19: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/zstd_decompress.cpp:180:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
2.16.0 bowtie2-2.5.4/zstd_decompress.cpp:97:24: debug: analyzeConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
head bowtie2-2.5.4/zstd_decompress.cpp:97:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]


DONE